"Harris A. Jaffee" <hjaffee@jhmi.edu> schrieb am 24.05.05 16:29:56: > You seem to have submitted 3 identical hgu133 files (with the methods > specified differently). They were all assessed successfully, as you > can see in the table: > > http://affycomp.biostat.jhsph.edu/AFFY2/TABLES.hgu/0.html#table133 yes. They are correct. > I don't know why your 4th submission failed assessment: I wanted to use my csv file instead of hgu133.csv (as standard example). I assume that I does not produce my csv file correctly. I cannot understand, where the problem lies. I use the following instructions: library(affy) library(tools) library(affycomp) # 42 Experiment data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL", ... "./R/ME_cel/Expt1_R2.CEL", "./R/ME_cel/Expt14_R3.CEL") my.Data <- expresso(data.raw, bg.correct = F, normalize = F, pmcorrect.method = "pmonly", summary.method = "medianpolish") x <- exprs(my.Data) write.table(data.frame(x,check.names=FALSE),file="./R/excel/ME_133_1.c sv",sep=",",col.names=NA,quote=FALSE) and then I receive in affycomp.R for ME_133_1.csv as my example: > Error in "[.data.frame"(s, , rownames(pData(pd))) : > undefined columns selected > Execution halted How can I produce correct csv file from CEL files? > Can I remove some/all of the duplication? Yes, please. I wanted to ask from you about it. best regards, Mohammad