Expression Parameters Accumulative Proportion of Variation Add Mean Difference filter to select significant tests Additional Bandwidth on Each Side of Tracks Additional PROC MIXED Statements Adjust Counts by Total Counts Adjustment Effects Allele Variable Alpha Alpha Values Annotation Chromosome Variable Annotation Label Variable Annotation Merge Variables Annotation Merging Variable Annotation Position Variable Annotation SAS Data Set Annotation Title Variables Annotation Variables to Keep Apply Certain Samples as Reference Apply data from autosomes for normalization Apply kernel density estimation for MA plot Apply normalized data for MA plot Apply reference baseline from previously input data set Array Standardization Method Apply weighting approach for trimmed mean Array Variables to Plot Bandwidth Multiplier of x-Dimension Bandwidth Multiplier of y-Dimension Baseline Baseline in Reference SAS Data Set Baseline Quantification Baseline reference data is log-transformed Baseline Reference SAS Data Set Baseline Value Baseline Variable Batch Profile Input SAS Data Set Biomaterial Provider Block Variable By Variable By Variables By Variables for Loess Normalization Variables by Which to Merge Annotation Data 1 Variables by Which to Merge Annotation Data 2 Calculate the absolute value of the differences Catalog Number Censor Variable Center rows Characteristics Chromosome Variable Class Variables Cluster significant LSMean profiles Cluster significant Mean profiles Coating Color Scale Color Variable Color Variables Column to Identify Control Rows in the EDDS Columns by Which to Merge with Input SAS Data Set Columns Defining Batches Component Output Data Set Name Compute Component Fixed-Effect Tests Compute Multiple Testing Adjustment Separately for Each Test Compute Pearson covariances instead of correlations Compute results for annotated rows only Compute results for secondary annotated rows only Constant to Apply Constants for Each Variance Component Contributors Control Levels Control Set Design Control Set Summary Statistic Coordinate Data Set Coordinate Merge Variables Covariates Create JMP Surface plot Cumulative Proportion of Variation to Explain Data Processing Data Set Containing LSMeans Differences to Include Data Set to Use for Filter Delete nonmatching rows Delete rows Delete rows not in First Tall Data Set Delete rows with at least this percentage of Missing values Delete rows with Interquartile Range satisfying this expression (use keyword IQR) Delete rows with Mean satisfying this expression (use keyword MEAN) Delete rows with Median satisfying this expression (use keyword MEDIAN) Delete Rows with number of missing values satisfying this expression (use keyword NMISS) Delete rows with Percentile satisfying this expression (use keyword PCTL) Delete rows with Standard Deviation satisfying this expression (use keyword STD) Density Smoothing Bandwidth Computation Method Density Smoothing Bandwidth Multiplier Description Design-Level By Variables Design-Level Grouping Variables Direction of the Cutoff Display Cumulative Percentage of Summary plots Display detailed distribution statistics and histograms Display Format for Density Grid Points Display side-by-side box plots Display Scatterplot matrices Display Standard Deviation versus Mean plots Distribution Distribution of Data DNA data is log-transformed DNA Design Variables to be Added in Output Data Sets DNA Intensity Input SAS Data Set DNA Matching Variables Effect Sizes Experimental Design SAS Data Set Experimental Design Data Set Corresponding to Baseline Reference Data Set Experimental Design SAS Data Set of DNA Intensity Experimental Design SAS Data Set of RNA Intensity Experimental Factor Variables Exponential Multiplier of Kernel Density Extract Protocol Feature Variable Fifth Experimental Design Data Set Fifth Tall Data Set File Containing Estimate Statements Filter data with Zero or Missing values Filter Rows Whose Proportion of Zero/Missing Values Exceeds this Cutoff Filter to Include Annotation Rows Filter to Include Observations Filter to Include Rows Filter to Include Secondary Annotation Rows Filtered Output Data Set Name Filtration Method for Data Points with Large Residuals First Experimental Design Data Set First Tall Data Set Fixed Effects Flagging Output Data Set Name Folder of Raw Data Files Folder of Track Settings Files Format Fourth Experimental Design Data Set Fourth Tall Data Set GenBank Accession Variable Gene Description Variable Gene Length Data Set Gene Length Variable Gene or LocusLink ID Variable Gene Symbol Variable Gradient Convergence Criterion [1,1000000] Group Percentage for Deletion Growth Protocol Hyb Protocol ID ID Variable In Mean plots, size Error Bars using: Include adjusted p-values in addition to -log10 (p-values) Include exponentiated Estimates and Differences Include Fold Changes in Addition to Log Fold Changes Include Fold Changes in Addition to Log2 Fold Changes Include group statistics in Output Data Set Include simple LSMean Differences only Include p-values in addition to -log10 (p-values) Include Standard Errors Include t-Statistics Input data is log-transformed Input SAS Data Set Input x and y Data Set Input z Data Set Intensity Columns to Filter JMP Journal Output File JMP Script Output File Name JSL Output File Keep 0 Values without normalizing Kenward-Roger Degrees of Freedom Method Key Variable(s) to Associate with Input SAS Data Set Key Variable(s) to Merge with Input SAS Data Set Key Variables for Merging Label Label Protocol Label Variable Lambda Number Link Function List all model fits List every model fit List-Style Specification of Intensity Columns to Filter List-Style Specification of Variables List-Style Specification of Variables for Which to Display Distributions List-Style Specification of Variables to Be Standardized List-Style Specification of With Variables Loess Weight Data Set -log10(p-Value) Cutoff Log Transformation of Measurements Log transformed Output Data Set LSMeans Control Levels LSMeans Difference Set LSMeans Difference Set for Volcano Plots LSMeans Effects LSMeans Effect to Keep in the Normalized Data LSMeans Effect to Retain in the Normalized Data LSMeans Standardization Method Manufacturer Manufacturer protocol Match case for key variables Maximum Filtering Loops Maximum Number of Principal Components to Apply Maximum z Value Mean Difference Filter Cutoff Means Control Levels Means Difference Set for Volcano Plots Means Standardization Method Merge Annotation into Residuals Data Set Merge Key Variables Merge Key Variables to Associate with Input SAS Data Set Minimum Distance Between Genotyping Groups Minimum Ratio Range Between 2 Homozygous Groups Minimum z Value Mixed Model Expression Index Output Data Set Name Mixed Model Output Data Set Name Mixed Model Output Data Set Prefix MMEI Output Data Set Name Molecule Multiple Testing Fixed Effects Multiple Testing Method Multipliers of Design Size New Batches from Previous Batches Normalized Response Filter Expression Number of By Groups to Process at a Time Number of Clusters Number of Density Grid Points Number of Discrete Classes to Use in Plots Number of Factors to Subtract from the Data Number of the First Principal Component for VCA Number of First Principal Component to Model Number of Last Principal Component to Model Number of LOESS Iterations Number of PLS Components Number of Principal Components Number of Random Splits Number of Rows to Process at a Time Number of Standard Deviations in Error Bars Number of x Blocks Number of x Grid Points Number of y Blocks Number of y Grid Points Numerical Parameter for Advanced Standardization Methods Organism Organism(s) Origin Corner Other Columns to Include Output Batch Profile Data Set Output Coordinates Data Set Output Data Set Output Data Set Containing Filtered Data Output Data Set for Graphs Output Data Set Name Output Data Set for MA Plot Output Data Set of KDMM Factors Output Data Set of Rescaling Factors Output Data Set of RPM Factors Output Data Set of TMM Factors Output Data Set of TPM Factors Output Data Set of Upper Quartile Factors Output Data Set Prefix Output Eigenvalues Data Set Output Experimental Design Data Set Output File Primary Title Output File Secondary Title Output Folder Output HTML File Output Normalized Data Set Output experimental samples only Output Plotting Data Set Output Ratio Data Set Output Statistics Data Set Output Surface Data Set Output Tall Data Set Output Test Data Set Output Updated Batch Profile Data Set Output Variance Components Data Set Overall Design Overlay density estimates PCA Plot Grouping Variables PDF or RTF Output File PDF or RTF Output File Name Percentage of Data to Be Included in Training Data Percentile to Compute for PCTL Statistic Percentage of Data on A Component to Be Trimmed Percentage of Data on M Component to Be Trimmed Percentage of Data to Be Trimmed before Summary [0,50] Percentage of Nonmissing and Nonzero Data to Be in Training Subset Percentile to Impute Perform log2 transform after standardization Perform within-array Loess normalization Platform Platform Contributors Platform Data Set Platform Organism Platform Title Plot Rate Plot standardized residuals Plot Variable 1 Axis Label Plot Variable 2 Axis Label Plotting Variables Position Variable Prefix for Experimental Design Output Data Set Names Prefix for Tall Output Data Set Names Primary Title to use in Plots PROC FACTOR Options PROC GLIMMIX Options PROC MIXED Options PROC MIXED/GLIMMIX Statements PROC PLS Options PROC MIXED Statements Pseudo-Likelihood Convergence Criterion PubMed ID QC Data Set Random Effects Random Number Seed Random Number Seed for Picking Random Subset Randomly split the data Ratio Output Data Set Raw Data File(s) Reference Variable Reference Variable to Be Applied as the Baseline Remove duplicate columns Repeats Replace intensities falling at least this many Standard Deviations above the Column Mean Replace intensities falling at least this many Standard Deviations below the Column Mean Replace intensities falling above this column percentile Replace intensities falling above this value Replace intensities falling below this Column Percentile Replace intensities falling below this value Replace highest values Replace lowest values Rescale the data based on the total measurements in the Training data set Residual Cutoff Residual False Positive Rate Response Filter Expression Response Variable Axis Label Result Data Set RNA data is log-transformed RNA Design Variables to be Added in Output Data Sets RNA Intensity Input SAS Data Set RNA Matching Variables RNA Output Data Set Round normalized count data to integer Row Index Variable Row-Level Class Variables Sample Description Sample Name Scale rows Scaling Approach Scan Protocol Second Experimental Design Data Set Second Tall Data Set Secondary Annotation Chromosome Variable Secondary Annotation Label Variable Secondary Annotation Merge Variables Secondary Annotation Position Variable Secondary Annotation SAS Data Set Select Training subset based on Missing status Separate and journal results by chromosome Separate results based on Design-Level By Variables Series Title Series Variables Server Output Directory Set flagging data to Missing Set negative values to Missing before imputing Shifting Factor Shrink variances using Empirical Bayes Smoothing Bandwidth Multiplier Smoothing Parameter SNP ID Variable Sort VCA Plots by Weighted Average Proportion of Variation Source Name Split by these variables Standardization Method Standardization Statistics Input SAS Data Set Standardize Standardize Batch profile Standardize KDMM factor Standardize TMM Scaling Factor Standardized Residuals Output Data Set Name Statistic to Impute Study Sub-Feature Variable Subject Variable Subset Data Set to Use for Normalization Summary Summary Statistic Support Technology Third Experimental Design Data Set Third Tall Data Set Threshold Time to Event Variable Title Track Settings Files Transposed Output Data Set Treatment Protocol Type of Correlation Type of Data Unbounded Variance Component Estimates Uniformly scale histograms in Detail plots Uniformly scale y-axes in Volcano and Chromosome Position plots Uniformly scale y-axes in Volcano plots Use pooled Estimate of Variance Value Definition Value of Columns above to Be Associated with Control Value of Columns above to Be Associated with Non-autosomes Value of Columns above to Be Associated with Reference Value of the Censor Variable that Indicates Censoring Value of Variable Above to Be Used as Denominator Value to Use to Replace Highest Values Value to Use to Replace Lowest Values Values of ID Variable to Plot Variable Containing Names of Loess Weight Data Set Columns Variable Defining the Ratio Variables Variables by Which to Merge Annotation Data Variables By Which to Merge Filter Data Set Variables by Which to Merge Primary Annotation Data Variables by Which to Merge Secondary Annotation Data Variables Defining Analysis Groups Variables Defining Blocks Variables Defining Control Sets Variables Defining Groups Variables Defining Groups for Mean Processing Variables Defining the One-Way Classification Variables for Which to Display Distributions Variables to Be Normalized Variables to Be Standardized Variables to Keep in Output Variables to Keep in Output or By Which to Merge Annotation Data Variance Component Effects Variables to Include in the Imputation Process Weblink Weighted With Kernel Density Where Clause for Subsetting Input Data Set in Test Run Winsor Rate With Variables Within Sub-Feature Median x-Coordinate Variable y-Coordinate Variable z-Coordinate Variables