Error: The copy number probe and SNP files do not have the same number of patients in them

This error occurs when you're trying to process Affymetrix 5.0 and 6.0 CEL files for copy number analysis and the proper library files (with a *.cdf extension) have not been selected. The newest Affymetrix library files contain both SNP and CNV probes. Previous versions only contained SNP probes.

Similar to Affymetrix marker maps, the latest Affymetrix library files can be downloaded using the NetAffx service in HelixTree. To download library files, select >Tools >Download Affymetrix Library File from the Project Navigator window. You will be prompted for your Affymetrix NetAffx login information, which can be freely obtained by registering on Affymetrix’s website.

https://www.affymetrix.com/analysis/netaffx/index.affx

Upon submitting this information, HelixTree will load a list of Affymetrix's most recently published library files for each of its chip sets. 

Select the appropriate files from the upper window (e.g. GenomeWideSNP_5.cdf) , and click Download. The file(s) will automatically be downloaded to the ../ HelixTree/AffyLibraryFiles directory.