JMP Genomics Files are Identified by Suffixes

Typical analyses in JMP Genomics often generate a large number of output files and data sets. This is especially true when input and output files are contained with the same folder, when a process produces multiple output files, or when the same output folder is used for multiple processes. If any or all of these conditions occur, the number of files in a folder can multiply dramatically. How do you identify and distinguish between the different files? More importantly, how do you prevent overwriting existing files with the output of subsequent processes, particularly when all of the files tend to be similarly named?

JMP Genomics adds a unique suffix to each output file generated by a process. Suffixes are specific to each process and are dependent on the type of content contained in the file. These suffixes enable you to identify different output files and to correlate them with specific processes. All of the suffixes used by JMP Genomics are listed alphabetically in the table below. Each suffix is defined both by the process that generates it and by the contents of the file that carries it.

Note: Even with the suffixes, it is still possible to overwrite existing files. You should take care to specify different names for output files when doing multiple runs with the same input files. Alternatively, you can specify different output folders.

JMP Genomics Files have suffixes: Identification of output files by suffix, process, and contents.

File Suffix

Processes Generating the File

Function/Contents of the File

_aag

•

Create Annotation Analysis Group Variables

Output data set listing the input data plus the annotation analysis group variable

_afr

•

Marker Properties

Output data set containing allele frequencies

_afreqs

•

Marker Properties

Output data set containing allele frequencies

_agc

•

Correlation and Grouped Scatterplots

Output data set consisting of the input data merged with the annotation data set

_ags

•

Correlation and Grouped Scatterplots

Output data set containing correlation statistics for each experimental group array pair

_alp

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_amc

•

ANOVA

•

Mixed Model Analysis

Output data set listing response and standardized residuals for each transcript cluster

_amr

•

ANOVA

Output data set listing annotation information and various statistics for the most significant markers

_amr_sig

•

ANOVA

Output data set containing the significant differences

_an0

•

Recombination and Linkage Groups

Output data set listing the markers (and their positions) found on each chromosome

_anm

•

ANOVA Normalization

Output data set with the same structure as the input data set but with normalized response variables

_anmbody

•

ANOVA Normalization

Output HTML body content

_anmcontents

•

ANOVA Normalization

Output HTML table of contents

_anmframe

•

ANOVA Normalization

Output HTML incorporating the body and table of contents

_ann

•

Copy Number/LOH Control Set Adjustment

•

Copy Number Partition

Output data set containing annotation information

_api

•

Array Pseudo Image

Output data set listing the X- and Y-coordinates, probeset IDs, and intensities for each spot on the specified array

_ars

•

ANOVA

•

One-Way ANOVA

•

Mixed Model Analysis

Output data set listing standardized residuals for each observations in the input data set

_as

•

Relationship Matrix

Output data set listing the relationship matrix generated using the allele sharing similarity estimate

_asf

•

Allele Specific Expression Filter

Output data set containing the filtering results

_asl

•

Allele Specific Expression Filter

Output data set containing the design and ID variables, DNA and RNA matching variables, genotype group, and log ratio data of DNA and RNA

_asp

•

Affected Sib-Pair Tests

Output data set containing affected sib-pair test statistics and .jsl file for plotting p-values

_asp_sbg

•

Affected Sib-Pair Tests

Output data set listing the number of significant markers for the selected affected sib-pair tests

_asr

•

Allele Specific Expression Filter

Output data set containing the log-ratio of RNA intensity data for estimated homozygous genotypes

_atan

•

ArrayTrack

Annotation file created by ArrayTrack

_bin

•

Copy Number Bin

Output data set listing the bins into which the probesets have been grouped. This data set also lists the physical position of the bin start site and the average intensity across the bin.

_binned

•

Spectral 2D Bin

Output binned data

_bnm

•

Batch Normalization

Output data set containing the batch-normalized data

_bnp

•

Batch Normalization

Output data set containing the results of the principal components analysis

_bns

•

Batch Normalization

•

Batch Scoring

Output data set containing mu and standard deviation across batches

_body

•

SNP Power

•

Marker Properties

•

Haplotype Estimation

•

htSNP Selection

•

Feature Flagger

Output HTML body content

body

•

Mixed Model Normalization

Output HTML body content

_Body

•

Check Data Contents

Output HTML body content

_bowa

•

Bivariate One-Way ANOVA

Output data set containing annotation data, and statistics on individual experiments and pair-wise comparisons

_box

•

Distribution Analysis

Output data set listing the relative densities of spots on each array grouped by similar responses; used for drawing box plots

_bsb

•

Batch Scoring

Output data set containing mu and standard deviation across batches

_bsc

•

Batch Scoring

Output data set containing the batch-normalized data

_cca

•

Case-Control Association

Output data set containing case-control association test statistics and .jsl file for plotting p-values

_ce

•

Combine Experiments

Output data set generated from the merging of multiple tall SAS data sets

_ceb

•

Column Enrichment

Output data set listing the categories that show results displaying significance as specified by the binary significance variables

_cec

•

Column Enrichment

Output data set listing the categories that show results displaying significance as specified by the continuous significance variables

_ceexp

•

Combine Experiments

Output experimental design data set

_cef

•

Column Enrichment

Output data set containing the Fisher Exact test results for the binary significance variables

_cep

•

Column Enrichment

Output data set containing PAGE results for the continuous variables.

_chrm

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_cim_out

•

QTL IM and CIM Analysis

Output data set listing position and associated LOD scores for each marker

_clm

•

Compare Linkage Maps

Output data set containing map, linkage group, marker, distance, and other matching and ordering information

_cml

•

QTL IM and CIM Analysis

Output data set listing the control markers used in the analysis

_cna

•

Copy Number/LOH Control Set Adjustment

Output data set containing marker, location, and other annotation information

_cnae

•

Copy Number/LOH Control Set Adjustment

Output data set containing experimental design information

_cnp_indata

•

Copy Number Partition

Output data set containing input annotation data with additional output columns

_contents

•

SNP Power

•

Marker Properties

•

Haplotype Estimation

•

htSNP Selection

•

Feature Flagger

Output HTML table of contents

contents

•

Mixed Model Normalization

Output HTML table of contents

_Contents

•

Check Data Contents

Output HTML table of contents

_cor

•

Correlation and Principal Components

•

Cross Correlation

Output data set listing the correlation of all the different variables in the input data

_cov

•

Correlation and Principal Components

Output data set listing the covariates of all the different variables in the input data

_cpg

•

SNP-Trait Association

•

Imputed SNP Trait Association

•

Q-K Mixed Model

•

Marker-Trait Association

•

SNP-SNP Interactions

Output data set containing covariance parameter estimates for the genotype test. This data set is generated whenever any random effects are specified.

_cpt

•

SNP-Trait Association

•

Imputed SNP Trait Association

•

Q-K Mixed Model

•

Marker-Trait Association

•

SNP-SNP Interactions

Output data set containing covariance parameter estimates for the trend test. This data set is generated whenever any random effects are specified.

_csn

•

Control Set Normalization

Output data set containing the normalized data

_csne

•

Control Set Normalization

Output experimental design data set

_dap

•

Append

A concatenated data set resulting from appending the rows of two different data sets

_data

•

Exon and Whole Transcript Expression CEL

SAS data set containing the imported data

_dc

•

Difference Chooser

Output data set containing LSMeans differences. Useful in ANOVA-related processes.

_den

•

Distribution Analysis

Output data set used for plotting the overlaid kernel density estimate plot

_det

•

Spectral 2D Peak Find

Output data set containing detailed information for each peak

_dge

•

Distribution Analysis

Output experimental design data set when using Group variables

_dgm

•

Distribution Analysis

Output data set when using Group variables

_dlb

•

Change Labels

Output data set in which the variables of the original data set have been relabeled

_dln

•

Change Lengths

The output data set in which the lengths of the variables of the original data set have been resized

_dmg

•

Merge

The large data set resulting from merging two smaller data sets

_dmt

•

Distance Matrix

Output data set listing the measures of dissimilarity between all pairs of observations in the experiment

_drk

•

Rank Rows

The output data set in which the individual values within each variable have been replaced with the ranking of that observation within the variable

_drn

•

Rename

The output data set in which the primary variables of the original data set have been renamed

_dro

•

Reorder

The output data set in which the order of the variables in the original data set has been changed

_drs

•

Statistics for Rows

Data set listing row-wise statistics for the primary data set. Rows meeting the criteria specified in the Delete Rows Satisfying this Expression box on the Options tab are excluded from the data set.

_dsa

•

Discriminant Analysis

Output data set containing all of the data from the input data set plus three additional columns. These include observation number, and two columns listing the predicted values for the dependent class variable.

_dsav

•

Discriminant Analysis

Lists the names of the variables selected and used for making predictions

_dsm

•

Statistics for Columns

Data set listing summary statistics for the variables in the primary data set

_dso

•

Distance Scoring

Lists the statistics and associated predictions for each of the individuals in the input data set

_dsov

•

Distance Scoring

Lists the names of the variables selected and used for making predictions

_dsp

•

Data Step

The modified data set resulting from executing SAS data step commands on a data set

_dss

•

Subset

Output subset data set

_dst

•

Sort Rows

The output data set in which the variables in the input data set have been sorted according to specified key variables

_dt

•

Spectral 2D Detrend

Output detrended data set

_dtf

•

Transform

The output data set resulting from the mathematical transformation of specified variables in a primary data set

_dtr

•

Transform Rectangular

The data set resulting from the transposition of a block of variables in the original data set

_eg

•

Expand Multiallelic Genotypes

Output data set with multiallelic genotypes expanded into one column per allele

_eg_anno

•

Expand Multiallelic Genotypes

Output annotation data set associating expanded genotype markers with markers

_eig

•

Correlation and Principal Components

•

Relationship Matrix

Output data set listing the Eigenvalues and associated experimental statistics

_eigenval

•

PCA for Population Stratification

Output data set containing eigenvalues and cumulative variance for PCs

_esc

•

Gene Set Scoring

Output data set containing the scored data

_est

•

Estimate Builder/Compare Means

Output file containing the estimate statements

_exp

•

Many different input engines, data set utilities and analytical processes

Experimental Design Data Set (EDDS)

_ffi

•

Feature Flagger

Output data set in which individual values for the variables have been replaced with "0", if values are within defined parameters, or "1", if values are outside of those parameters

_fin

•

Filter Intensities

Output data set listing the filtered intensities

_fnm

•

Factor Analysis Normalization

Output data set with the same structure as the input data set, but with normalized response variables

_fp

•

Meta-Analysis

•

GWAS Meta-Analysis (Forest Plot action button)

Output data set containing statistics for forest plot

_frame

•

SNP Power

•

Marker Properties

•

Haplotype Estimation

•

htSNP Selection

•

Feature Flagger

Output HTML incorporating the body and table of contents

frame

•

Mixed Model Normalization

Output HTML incorporating the body and table of contents

_Frame

•

Check Data Contents

Output HTML incorporating the body and table of contents

_fs

•

Flip Strand

Output annotation data set containing corrected strandedness for major/minor alleles

_gea

•

GxE Interaction

Output data set containing ANOVA statistics

_gee

•

GxE Interaction

Output data set containing stability statistics

_gel

•

GxE Interaction

Output data set containing genotype LS means

_gem

•

GxE Interaction

Output data set containing GxE LS means

_gen

•

GxE Interaction

Output data set containing ANOVA from linear-bilinear model

_gep

•

GxE Interaction

Output data set containing PCA statistics

_ges

•

GxE Interaction

Output data set containing scree plot statistics for PCs

_gfr

•

Marker Properties

Output data set containing genotype frequencies

_gfreqs

•

Marker Properties

Output data set containing genotype frequencies

_glm

•

General Linear Model Selection

Lists the statistics and associated predictions for each of the individuals in the input data set

_glmv

•

General Linear Model Selection

Lists the names of the variables selected and used for making predictions

_gma

•

GWAS Meta-Analysis

•

Meta Analysis

Output data set containing meta-analysis p-values and heterogeneity statistics

_gma_sbg

•

GWAS Meta-Analysis

Output data set listing the number of significant markers for the selected association tests

_gms

•

Gene Model Summary

Output data set containing the summarized data

_gp

•

Build Genotype Probability Data Set

Output data set listing the probabilities of observing specific QTL genotypes at each one cM interval along the chromosome(s)

_gse

•

Gene Set Enrichment

Output data set containing enrichment test results

_gsei

•

Gene Set Enrichment

Output data set containing 0-1 indicator variables for the categories

_gtt

•

Hy’s Law Screening

Graph Time Trends drill down data set.

_hc

•

Hierarchical Clustering

Output data set containing all of the variables from the input data set plus results (row means and standard values, the cluster to which each belongs and its place within the cluster) of the hierarchical clustering

_hest

•

Haplotype Estimation

.html output files, .jsl file for plotting p-values, and output data set containing association test statistics

_hfr

•

Haplotype Estimation

Output data set containing haplotype frequency estimates that can be used as input to the htSNP Selection process

_her

•

Haseman-Elston Regression

Output data set containing Haseman-Elston regression test statistics and .jsl file for plotting p-values

_her_sbg

•

Haseman-Elston Regression

Output data set listing the number of significant markers for the tests

_hph

•

Haplotype Estimation

Output data set containing phase assignment probabilities. This data set can be used as the input data set for the Haplotype Trend Regression process.

_hrg

•

Haplotype Trend Regression

Output data set containing dependent variables, window, and F-statistic information.

_hrs

•

Haplotype Trend Regression

Output data set containing dependent variables, haplotype and name, window, and F-statistic information.

_hti

•

htSNP Selection

Output data set that contains all the columns from the annotation data set with an additional htSNP Indicator column

_htr

•

Haplotype Trend Regression

.html output files

_hts

•

htSNP Selection

.html output files, .jsl file for displaying htSNPs, and output data set containing htSNP information

_hwe

•

Marker Properties

Output data set containing HWE test statistics and other marker properties

_hwe_sbg

•

Marker Properties

Output data set listing the number of significant markers for the HWE test

_hwetest

•

Marker Properties

Output data set containing HWE test statistics and other marker properties

_ibd

•

Relationship Matrix

Output data set listing the relationship matrix generated using the identical by descent estimate

_ibs

•

Relationship Matrix

Output data set listing the relationship matrix generated using the identical by state estimate

_igp

•

Imputed SNP (Wide Format)

•

Imputed SNP (Tall Format)

Stacked output genotype probabilities SAS data set containing probabilities for each genotype at a SNP

_igt

•

Imputed SNP (Wide Format)

•

Imputed SNP (Tall Format)

Output genotype threshold SAS data set listing the most likely genotype for each SNP

_ipm

•

Marker Properties

Output data set containing the proportion of missing genotypes

_iqr

•

Data Standardize

Output data set containing the IQR standardized values for the input data set

_isr_N

•

IBS Sharing Regions

Output data set for chromosome N in tall format with sample genotypes, IBS sharing count, and run statistics

_iss

•

IBS Sharing Regions

Output data set with lengths and spans of runs across all chromosomes

_ist

•

Imputed SNP-Trait Association

Output data set containing association test statistics and .jsl file for plotting p-values

_ist_sbg

•

Imputed SNP-Trait Association

Output data set listing the number of significant markers for the selected association tests

_itt

•

IBS Sharing Regions

Output data set

_jnm

•

Output data set containing SU normalized data

_jnp

•

Output data set listing the four estimated parameters for each array used to generate the SU normalized data

_kc

•

K Matrix Compression

Output data set containing the compressed matrix

_kcf

•

K Matrix Compression

Output data set containing the criteria for optimal compression level, the corresponding values, and number of clusters generated during the compression

_kcv

•

K Matrix Compression

Output data set containing the covariance parameter estimates from every model fit during the compression

_kmc

•

K-Means Clustering

Lists the center of each cluster and the corresponding statistics

_kmd

•

K-Means Clustering

Lists the statistics for each observation, the cluster to which the observation has been assigned, and its distance from the cluster mean.

_kmf

•

KDMM Normalization

Output data set containing KDMM scaling factor and total mapped reads for each sample

_kml

•

KDMM Normalization

Output data set containing log-transformed KDMM normalized data

_kmm

•

KDMM Normalization

Output data set containing KDMM normalized data

_kmp

•

KDMM Normalization

Output data set containing A and M component, and kernel density, for each sample

_kmx

•

Kinship Matrix

Output data set consisting of the input data modified to identify the parents of the different pedigrees and matrix statistics

_knn

•

K-Nearest Neighbors

Lists the statistics and associated predictions for each of the individuals in the input data set

_knnv

•

K-Nearest Neighbors

Lists the names of the variables selected and used for making predictions

_ld

•

Linkage Disequilibrium

.jsl file for displaying LD results

_ldbb

•

LD Block Creation

Output data set listing detailed LD block information (first and last marker and location, and block size and length) for every block in every chromosome

_ldbc

•

LD Block Creation

Output data set listing the name, location, LD block, and annotation information for each of the SNPs

_ldbs

•

LD Block Creation

Output data set listing Dprime, locus, distance, AbsDprime, and other information for every pair of markers

_ldbs_N

•

LD Block Creation

Output data set listing Dprime, locus, distance, AbsDprime, and other information for every pair of markers within annotation group variable N (for example, chromosome)

_ldc

•

Linkage Disequilibrium

Output data set containing LD measures used in the Contour Plot and/or the LD Decay plot

_ldc_N

•

Linkage Disequilibrium

Output data set containing LD measures used in the Contour Plot and/or the LD Decay plot, within annotation group variable N

_ldm

•

Linkage Disequilibrium

Output data set containing haplotype, frequency, D, correlation coefficient, Dprime, delta, and other statistics for each pair of markers

_lds

•

Linkage Disequilibrium

Output data set containing LD test statistics

_lds_N

•

Linkage Disequilibrium

Output data set containing LD test statistics within annotation group variable N

_ldts

•

LD tagSNP Selection

Output data set containing tagSNP information

_ldts_body

•

LD tagSNP Selection

.html output file summarizing the tagSNP information

_len

•

List Enrichment

Output data set containing the list enrichment statistics

_lgr

•

Logistic Regression

•

SNP Interaction Discovery

•

Recombination and Linkage Groups

_lgrv

•

Logistic Regression

•

SNP Interaction Discovery

Lists the names of the variables selected and used for making predictions

_lite

•

Copy Number Partition

Output data set containing physical position, sample, chromosome, segment start and end, intensity information, and other statistics

_lkmp

•

Linkage Map Viewer

Output data set containing marker name, linkage group, original and map order, distance, and other information

_lmo

•

Linkage Map Order

Output data set containing marker name, linkage group, original and map order, distances, and other order statistics

_lmr

•

Linkage Map Order

Output data set containing marker pairs, recombination rate, linkage group, locus, and other information

_lnm

•

LoessNormalization

Output data set containing the loess normalized data

_lnp

•

Loess Normalization

Output data set containing data used for drawing the M-A plots

_lsm

•

SNP-SNP Trait Association

•

Pleiotropic Association

•

Q-K Mixed Model

•

SNP-SNP Interactions

Output data set containing genotype LS means and differences

_map

•

Imputed SNP (Tall Format) Input Engine

Output data set containing annotation marker map information

_mcp

•

Multiple SNP-Trait Association

Output data set containing multiple-locus regression covariance estimates

_mcpp

•

Multiple SNP-Trait Association

Output data set containing PCA regression covariance estimates

_mdf

•

Multidimensional Scaling

Output data set listing statics from the multidimensional scaling process

_mdr

•

Multidimensional Scaling

Output data set listing the statistics for and distances between pairs of observations from the input data set

_mds

•

Multidimensional Scaling

Output data set listing the multi-dimensional coordinates of each observation

_mea

•

Data Standardize

Output data set containing the mean standardized values for the input data set

_med

•

Data Standardize

Output data set containing median standardized values

_meds

•

Data Standardize

Output data set containing location and scale estimates used to median-center the input values

_metadata

•

Copy Number Partition

Output metadata table.

_mgs

•

Missing Genotype by Trait Summary

Output data set listing the counts of genotyped cases and controls, the number of missing genotypes for cases and controls, and the statistics for testing for different missing proportions between cases and controls for each marker

_mgs_sbg

•

Missing Genotype by Trait Summary

Output data set listing the number of significant markers for missing test, for each value of the annotation group variable

_mld

•

Malecot LD Map

.jsl file for creating plots and output data set containing estimates of LDU between pairs of markers

_mml

•

Malecot LD Map

Output data set containing estimates for parameters M and L

_mmp

•

Mixed Model Power

Output data set listing power values and associated t-statistics for a set of hypothesis tests for a range of alpha and effects sizes

_mmr

•

Mixed Model Analysis

Lists annotation and statistical information for each of the groups

_mmr_sig

•

Mixed Model Analysis

Output data set containing the significant differences

_mnm

•

Mixed Model Normalization

Output data set with the same structure as the input data set but with both the original and the normalized response variables

_mpe

•

Multiple SNP-Trait Association

Output data set containing multiple-locus regression parameter estimates

_mpep

•

Multiple SNP-Trait Association

Output data set containing PCA regression parameter estimates

_mrs

•

Mixed Model Analysis

Output residual data set

_msd

•

Merge Gene Sets

Output merged data set

_mst

•

Multiple SNP-Trait Association

Output data set containing association test statistics

_mtr

•

Merge and Transform

The output data set resulting from the merging of two sets sharing a common set of variables and the subsequent computation of an arbitrary function for each pair of variables sharing the same name

_mta

•

Marker-Trait Association

Output data set containing association test statistics and .jsl file for plotting p-values

_mta_sbg

•

Marker-Trait Association

Output data set listing the number of significant markers for the selected association tests

_mvi

•

Missing Value Imputation

The complete output data set in which values missing from the input data set have been imputed from the non-missing values in the same row

_names

•

Nexus

Output data set containing names of markers

_num

•

Marker Properties

Output data set containing numerically coded genotypes used in subsequent processes

_numgeno

•

Marker Properties

Output data set containing numerically coded genotypes used for the cell plot

_numgeno (by default, or other Prefix for Column Names specified)

•

Recode Genotypes

Output data set with recoded genotypes

_one

•

Single Marker Analysis

Output data set listing the results of the regression analysis and -log2 p-values for association of each of the markers with each of the two quantitative traits, along with annotation information for each of the markers

_org

•

Q-K Mixed Model

•

SNP-SNP Interactions

•

SNP-Trait Association

Output data set containing residuals from genotype test

_ort

•

PCA for Population Stratification

•

Q-K Mixed Model

•

SNP-SNP Interactions

•

SNP-Trait Association

Output data set containing residuals from trend test

_owa

•

One-Way ANOVA

Output data set containing annotation data, and statistics on individual experiments and pair-wise comparisons

_owa_sig

•

One-Way ANOVA

Output data set containing the significant differences

_pca

•

Principal Components Analysis for Population Stratification

•

Principal Components Analysis

Output data set listing the row scores for each of the principal components

_pce

•

PCA for Population Stratification

Output data set containing EigenCorr statistics for PCs

_pcm

•

Principal Components Analysis for Population Stratification

Output data set containing the PCA data merged into the input data set

_peg

•

SNP-Trait Association

•

Survey SNP-Trait Association

•

Pleiotropic Association

•

Marker-Trait Association

•

SNP-SNP Interactions

Output data set containing the parameter estimates for the genotype test

_pet

•

SNP-Trait Association

•

Survey SNP-Trait Association

•

Imputed SNP-Trait Association

•

PCA for Population Stratification

•

Pleiotropic Association

•

Marker-Trait Association

•

SNP-SNP Interactions

•

QTL Single Marker Analysis

Output data set containing the parameter estimates for the trend test

_pi

•

Plot Intensities

Output data set containing raw intensities and row statistics for the input data set

_pla

•

Pleiotropic Association

Output data set containing association test statistics for MANOVA and individual trait tests

_pla_sbg

•

Pleiotropic Association

Output data set listing the number of significant markers for the selected association tests

_plr

•

SNP Interaction Discovery

_plrv

•

SNP Interaction Discovery

Lists the names of the variables selected and used for making predictions

_pls

•

Partial Least Squares

Lists the statistics and associated predictions for each of the individuals in the input data set

_plsv

•

Partial Least Squares

Lists the statistics associated with the ability of each marker to be used as a predictor for the dependent class variable

_pmd

•

Population Measures

Output symmetric matrix of dissimilarities between specified groups within a study

_pmf

•

Population Measures

Output data set listing the individual F-statistics for each marker

_pmg

•

Pleiotropic Association

Output data set containing MANOVA test statistics for genotype test

_pmo

•

Population Measures

Output data set listing the overall F-statistics for the population

_pmt

•

Pleiotropic Association

Output data set containing MANOVA test statistics for trend test

_pps

•

Principal Components Analysis for Population Stratification

Output data set listing each of the markers with selected annotation data and the resulting probabilities the markers are associated with the disease trait, given population stratification

_pnm

•

Effect Removal via PLS Normalization

•

Partial Least Squares Normalization

Output data set with the same structure as the input data set but with normalized response variables

_prs

•

Relationship Matrix

Output data set listing pairs of samples having an identical-by-descent value exceeding a specified threshold

_psc

•

Phenotype Summary

Output data set containing counts for categorical variables

_psq

•

Phenotype Summary

Output data set containing counts for quantitative variables

_ptr

•

Partition Trees

Output data set listing the input data that has been recursively partitioned to optimal splitting relationships as determined by the specified dependent and predictor variables

_ptrv

•

Partition Trees

Lists the names of the variables selected and used for making predictions

_pva

•

P-Value Adjustment

Output data set containing the columns in the input data set with four additional columns listing the adjusted p-values for each set of observations

_pvb

•

P-Value Browser

Output data set containing the columns in the input data set with four additional columns listing the adjusted p-values for each set of observations

_pvc

•

Correlation and Principal Components

Output data set containing the variance within each of the principal components that can be attributed to each of the variance components

_pvc

•

P-Value Combination

Output data set containing combined p-values

_qcbp

•

Exon and Whole Transcript Expression CEL

Output data set that is used to create a pseudoimage of the arrays

_qkm

•

Q-K Mixed Model

Output data set containing association test statistics and .jsl file for plotting p-values

_qnm

•

Quantile Normalization

Output data set containing the quantile normalized data

_qnp

•

Quantile Normalization

Output data set containing the quantile normalized data along with relative rank of each observation and residual data

_qtdt

•

Quantitative TDT

Output data set containing Q-TDT test statistics and .jsl file for plotting p-values

_qtdt_sbg

•

Quantitative TDT

Output data set listing the number of significant markers for the selected association tests

_rai

•

Ratio Analysis

Output data set containing the log intensities of the input data

_rar

•

Ratio Analysis

Output data set containing the log ratio of the two-channel input data

_ratio

•

Ratio Analysis

Output data set containing a condensed version of the input experimental design data set, reorganized in terms of the variable defining the ratio

_rbm

•

Radial Basis Machine

Lists the statistics and associated predictions for each of the individuals in the input data set

_rbmv

•

Radial Basis Machine

Lists the names of the variables selected and used for making predictions

_rm

•

Relationship Matrix

Data set containing the root matrix as computed by single value decomposition (SVD) appended to the input data set

_rmg

•

Recode Missing Genotypes

Output data with missing genotypes recoded to SAS missing values

_rpf

•

RPM Scaling

Output data set containing RPM scaling factor and total mapped reads for each sample

_rpl

•

RPM Scaling

Output data set containing log-transformed RPM normalized data

_rpm

•

RPM Scaling

Output data set containing RPM normalized data

_rules

•

Copy Number Partition

Output data set containing overall worth and rules data

_rva

•

Rare Variant Association

Output data set containing rare variant association test statistics

_s2b

•

2D Bin

Output data set containing the binned values for each variable

_s2d

•

2D Detrend

Output data set containing the baseline-adjusted and corrected values

_s2p

•

2D Peakfind

Output data set identifying each peak found in each trace

_s2p_det

•

2D Peakfind

Output data set providing specific information (upper and lower boundaries, height, area, for example) for each peak identified in each trace

_s2g

•

2D Plot

Output data set listing trimmed input values

_s3a

•

3D Align

Output data set listing the X and Y coordinates for each row with the Z values for each sample listed in a separate column

_s3g

•

3D Plot

Output data set listing the X and Y coordinates for each row with the Z values for each sample listed in a separate column

_sbg

•

Case-Control Association

•

PCA for Population Stratification

•

Marker-Trait Association

•

SNP-Trait Association

•

Imputed SNP-Trait Association

•

Survey SNP-Trait Association

•

Q-K Mixed Model

•

Quantitative TDT

•

TDT

•

GWAS Meta-Analysis

•

Multiple SNP-Trait Association

•

Rare Variant Association

•

Pleiotropic Association

Output data set listing the number of significant markers for the selected association tests

__sbg

•

Q-K Mixed Model

Output data set listing the number of significant markers for the selected association tests

_sdp

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_seq

•

Affymetrix Tiling CEL Input Engine

Output sequence data set

_sfg

•

SNP-Trait Association

Output data set containing survival function estimates for genotype test

_sfs

•

Surface Summary

Output data set containing the estimated surface

_sft

•

SNP-Trait Association

Output data set containing survival function estimates for trend test

_sgc

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_sgl

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_sma

•

QTL Single Marker Analysis

Output data set containing chromosome number and label, marker position and label, trait, effect, and several estimates and test statistics

_sma_sbg

•

QTL Single Marker Analysis

Output data set listing the number of significant markers for the trend test

_smc

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_snl

•

Affymetrix Cytogenetics CHP Input Engine

Output data set

_sp

•

Exon and Whole Transcript Expression CEL

Output data set that lists single-probes not associated to any probeset

_spmm

•

Survival Predictive Modeling

Output data set listing mean survival times

_spms

•

Survival Predictive Modeling

Output data set listing survival functions corresponding to the training data set

_spmt

•

Survival Predictive Modeling

Output data set listing survival functions corresponding to the test data set

_spmv

•

Survival Predictive Modeling

Output data set listing the effects applied in the Cox model

_sps

•

Exon and Whole Transcript Expression CEL

Output data set that lists single-probe-sets not associated to any transcript cluster

_sr

•

Subset and Reorder Genetic Data

The output data set resulting from the reordering/removal of markers or individuals from either a genotype or annotation data set

_sr_d

•

Subset and Reorder Genetic Data

The output annotation data set containing excluded markers only

_ssi

•

SNP-SNP Interactions

Output data set containing SNP-SNP association test p-values

_sst

•

Survey SNP-Trait Association

Output data set association test statistics

_sst_sbg

•

Survey SNP-Trait Association

Output data set listing the number of significant markers for the selected association tests

_sta

•

SNP-Trait Association

•

PCA for Population Stratification

Output data set containing association test statistics and .jsl file for plotting p-values

_sta_sbg

•

SNP-Trait Association

Output data set listing the number of significant markers for the selected association tests

_stacked

•

Copy Number Partition

Output data set containing sample, chromosome, physical position, intensity, segment start and end, and other information

_std

•

Data Standardize

Output data set with the same structure as the input data set but response variable values that have been standardized using one or more different methods

_stk

•

Stack

Output stacked data set

_sub

•

Check Data Contents

Output subset data set

_sumrules

•

Copy Number Partition

Output data set containing sample, chromosome, and position columns

_sumstats

•

Copy Number Partition

Output data set containing rules, intensity, and positioning columns

_sva

•

Survival Analysis

Output data set listing survival statistics

_svd

•

Calculate Square Root of Matrix

Output data set

_tal

•

Transpose Tall and Wide

•

Unstack

The tall data set resulting from either the transposition of a wide data set or the unstacking of a stacked data set. Note: These processes also generate an associated EDDS.

_tdt

•

TDT

Output data set containing TDT statistics and .jsl file for plotting p-values

_tdt_sbg

•

TDT

Output data set listing the number of significant markers for the selected association tests

_tdtt

•

TDT

Output data set containing a pair of allelic transmission scores for each individual at each marker locus

_tmf

•

TMM Normalization

Output data set containing TMM scaling factor and total mapped reads for each sample

_tml

•

TMM Normalization

Output data set containing log-transformed TMM normalized data

_tmm

•

TMM Normalization

Output data set containing TMM normalized data

_tmp

•

TMM Normalization

Output data set containing MA plot data

_tst

•

Correlation and Principal Components

•

Cross Correlation

Output data test data set containing the p-values for the test that the correlation equals zero

_uqf

•

Upper Quartile Scaling

Output data set containing upper quartile scaling factor and total mapped reads for each sample

_uql

•

Upper Quartile Scaling

Output data set containing log-transformed upper quartile normalized data

_uqs

•

Upper Quartile Scaling

Output data set containing upper quartile normalized data

_vc

•

Correlation and Principal Components

•

Batch Normalization

Output data set containing variance component estimates computed from the principal components

_vcp

•

Variance Components

Output data set listing each of the markers with selected statistics for the chi-square statistics and p-values for the likelihood ratio test or the z-scores and p-values for the Wald test that test for linkage between each marker and the quantitative trait

_vcp_sbg

•

Variance Components

Output data set listing the number of significant markers for the selected test

_vg

•

Verify Gender of Samples

Output data set listing the genetic sex of the individuals

_vgs

•

Verify Gender of Samples

Output data set listing the genetic sex of the individuals, without the marker variables

_wid

•

Transpose Tall and Wide

The wide data set resulting from the transposition of a tall data set

•

Surface Summary

Output coordinates data set