Output | Import | Illumina Copy Number Input Engine

Illumina Copy Number Input Engine
Running this process for the Illumina_CNV370_Samples_Confidential.txt example generates the Results window shown below. Refer to the Illumina Copy Number Input Engine process description for more information.
Note: For this example, R, X, Y, Log_R_Ratio, LOH_Score, and CNV_Value were specified in theColumns to Include option.
The Results window contains the following elements:
Output Data
This process generates the following data sets:
Intensity Data Set: (Also know as the Copy Number Data Set or the Output Data Set). This data set contains the data from the input file.
Experimental Design Data Set (EDDS): This data set lists specific information about experimental details for each of the arrays. Refer to Experimental Design Data Set (EDDS) for more information about this data set. Note: There can be more that one EDDS depending on the columns specified in theColumns to Include option. In this example a separate EDDS was generated for analysis of data in the Log_R_Ratio column.
XY Data Set: This data set contains the intensity data for the individuals in the sample. This data set only contains the X and Y measures (assuming that these measures are present in the text file exported from BeadStudio). This is a tall data set, with SNPs listed in rows, and individuals listed in the columns. There are two rows per SNP; one row lists the intensity value for X (the normalized intensity for the A allele) while the second row lists the intensity value for Y (the normalized intensity for the B allele). An Allele column in this data set identifies the allele whose intensity is listed in each row
XY EDDS: This data set lists experimental details needed for further analysis of the data contained in the XY Data Set.
Note: You can view the data in a file or data set by clicking either Open or View Subset (when the data set is very large).
Launch Follow-up Processes
Basic Copy Number Workflow: Click Basic Copy Number Workflow to launch the Basic Copy Number Workflow process with the output data set, EDDS, and annotation data set specified as input.
Click Reopen Dialog to reopen the completed process dialog used to generate this output.
Click Close All to close all graphics windows and underlying data sets associated with the output.