Jerry <norn2k at="" ...=""> writes: > > Hi, > ? > 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! > ? > Best, > Jianjun > > PS: The package I used is gcrma 2.12.1. I also observed similar results on?2.14 version. > > Hello, I'm running into the same problem with gcrma and justGCRMA. They are not giving the same numeric results. Is this an intended feature? I was under the impression that these two methods were identical with the exception that justGCRMA was more memory efficient because it didn't have to create an AffyBatch object. Can anyone shed some light on this subject? Thanks, Jin