
Hello all,   I am having trouble normalizing with gcrma package.   I start off with 4 Affy chip CEL files. I read them in, and then performed gcrma with default parameter. Then I made a boxplot of the normalized data. The result of the plot is tail underneath the 1st quartile is either very short or completely missing. The median for each assay, although lined up, is very close to the 1st quartile. Judging from the nature of the data, I know this is wrong. I also tested on the example Dilution data, and got the similar result as well (i.e. lower tail absent).
  My code is simply:DataWTPBS <-
ReadAffy(celfile.path="data/WTPBS/");
WTPBSgcRMA <-
gcrma(DataWTPBS);
boxplot(exprs(WTPBSgcRMA));   I've checked if any of my packages need to be updated. I also made the boxplot of unnormalized data and it looked fine.
  Any suggestion on why this might be the case?
Thank you!Sincerely,Casper
University of British Columbia 		 	   		  
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