I have CEL files from Cytoscan HD (n=39) as well as Affy GenomeWide SNP Array 6.0 (two populations, n=60 & n=500). I'd like to process these files using PennCNV to get copy number alteration information. Several papers have identified PennCNV as the best free pipeline to use for this analysis, which is why I want to use it.
I need to preprocess the files, but because I have so few in two groups, I cannot use PennCNV-Affy, because of the following comment:
" If the user has only a few CEL files, then it is necessary to use the default canonical clustering file in the PennCNV-Affy package, but in this case the CNV calls may not be reliable"
The only other package I've found that works to preprocess the files to prep for PennCNV is Aroma. (Note: affy2sv R package does not yet work if using the na33 reference genome which is why I can't use it). But I'm having issues figuring out how to output files necessary for PennCNV from Aroma.
So, my question:
1) Should I use Aroma to pre-process or take my chances with the PennCNV-Affy (which has no information on doing this with Cytoscan)?
2) If using Aroma, can anyone speak to how to output files for PennCNV with Aroma?