I am familiar with methods for detecting mosaicismusing Illumina array data, but it seems that there are far fewer tools for detecting mosaic regions in Affymetrix array data. There are a few tools that seem to attempt detection, but I was wondering if there were any others who found a solution that works well with Affymetrix data, or a detection method that allows control of false positive discovery rates?
I guess I'll answer my own question. What I ended up doing is running MAD (my first link in the question) using parameters that would yield a higher false discovery rate (FDR) for Illumina array data. This allowed me to detect large mosaic anomalies at a reasonable FDR, but still left room to lower the alpha and theta parameters to "discover" more anomalies at a higher FDR.
It seems that my original question is something that stems from inherent disparities in the quality of Illumina vs. Affymetrix B allele frequencies.
i'm totally new in this area, and i am wondering why all the method of detecting mosaic is based on data derived from Illumina but not from affymetrix. Are there any specific defection in the results of Affy?
