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Detection Of Mosaicism (Allelic Imballance) Using Affymetrix Gw6 Data?

I am familiar with methods for detecting mosaicism using 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?

affymetrix allele allele
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updated by chengwang29 • chengwang29 • written by Matt Shirley Matt Shirley

2 answers

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.

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written by Matt Shirley Matt Shirley

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?

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written by chengwang29 • chengwang29

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