Illumina Copy Number Input Engine

The Illumina Copy Number Input Engine imports copy number data from files generated by Illumina® BeadStudio software into a SAS data set that can be used as input for the advanced JMP Genomics analytical processes.

What do I need?

The Illumina Copy Number Input Engine can import data from either:

•	the Full Data Table produced by the BeadStudio Genotyping Module, or

•	the Final Report file generated by the BeadStudio Report Wizard.

The Full Data Table presents data in the tall format, having markers represented in rows and individual samples presented in columns. The Final Report file presents the data in a stacked format: each marker/individual pair is presented in a separate row. You can import various copy number metrics from both types of files, including log R Ratio and B Allele Freq. Additional information about the individual samples and marker annotation can be imported from the sample and map files.

The following example uses a proprietary data set provided by Illumina. These files, which include the Full Data Table.txt full data file, the Illumina_CNV370_Samples_Confidential.txt final report file, and the Samples Table.txt sample file, were saved to an Illumina folder saved in the JMP Genomics Sample Data folder. Please contact Illumina for more information about this data set.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the Illumina Copy Number Input Engine output documentation for detailed descriptions.