Step 1. Prepare a LogR DSF File

The first step in performing PBAT CNV association is to prepare a DSF file containing LogRs. Again, this tutorial will not cover this process as it is discussed in-depth in Steps 1-3 of the Whole Genome Copy Number Association Tutorial. The following ZIP file contains a sample DSF you use for this tutorial:

• 30common_pbat_cnv.zip (contains a LogR DSF file containing ~500k LogRs on 30 samples and a corresponding CSV pedigree spreadsheet)

NOTE: In order to properly match LogRs with pedigree information (covered in Step 3), you will need matching columns in both the LogR DSF file and the pedigree spreadsheet (Step 2). Processing Affymetrix CEL files using CNAM will automatically create a row label column in the resulting LogR DSF file with each row having Sample names consistent with the CEL file names.

For example, the screenshot below is of a LogR DSF created upon processing Affymetrix HapMap CEL files. Notice the first sample CEU_NA06985.cn. The CEL file name for this sample was CEU_NA06985.cn.cel. Upon creation of the DSF file, CNAM automatically made the row label the same as the CEL file name minus the *.cel extension. It is important for CNV analysis that there is a similar column in your pedigree spreadsheet that matches these Sample names in order for the software to properly match LogR data with pedigree information.