Dear All: I read 178 affy results into on object using ReadAffy(). however, when I tried to computer MAS, the computer apparently don't have enough memory to complete the operation. I wonder if there is anyway to circumvent this. Another question is after getting MAS, how do I write results to different file based on the origin of the tissue? I have all affy in MAS5 but in separate files, I wonder if I can use R to combine them based on their tissue origin, this is actually an alternative to what I asked above -- but I am no good with R. Best regards Hao Liu, Ph. D

With MAS5, you don't have to analyze all of your data at the same time (unlike most of the other methods in the affy package), so really all you need to do is combine the data based on tissue origin. It is simple to combine the data if you know which samples are a particular tissue type. Use the exprs() accessor function to extract the required columns from each of your exprSets. For instance, if you have three exprSets and the first five columns in each are a given tissue, you can combine into a matrix like this: first.tissue <- cbind(exprs(exprSet.one)[,1:5], exprs(exprSet.two)[,1:5], exprs(exprSet.three)[,1:5]) Where exprSet.one, etc are the names of your exprSets. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Hao Liu <liuha@umdnj.edu> 04/24/04 10:20 PM >>> Dear All: I read 178 affy results into on object using ReadAffy(). however, when I tried to computer MAS, the computer apparently don't have enough memory to complete the operation. I wonder if there is anyway to circumvent this. Another question is after getting MAS, how do I write results to different file based on the origin of the tissue? I have all affy in MAS5 but in separate files, I wonder if I can use R to combine them based on their tissue origin, this is actually an alternative to what I asked above -- but I am no good with R. Best regards Hao Liu, Ph. D _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor