[BioC] Discrepancy on results from gcrma function and justGCRMA

Jerry norn2k at yahoo.com
Tue Nov 4 08:25:32 CET 2008

I'm currently using gcrma package in R to summarize probeset intensities from CEL files. Surprisingly, I found that the results generated from gcrma function and justGCRMA function are quite different. In general, expression values from gcrma function are lower and the boxplots from gcrma are quite asymmetric (no tails on the bottom). I attached some plots below for your information. This confused me as I thought that the two functions implemented similar algorithms. 
Thank you so much for your help!

PS: The package I used is gcrma 2.12.1. I also observed similar results on 2.14 version.


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