I would like to have an idea on my FDR and I thought that the MULTTEST package will do it. I read the MULTTEST.pdf manual and it is quite clear how to run the golub.RData example file. The problem is on how to run MULTTEST in my arrays data. To begin, how do I make the *.RData file using my data? Which of my files do I use? It seems that I have to use the output file after using this R function: > eset <- expresso(Data,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish") I used then: > roger=exprs(eset) > roger.gnames=geneNames(eset) > roger.cl=treat > data(roger) > dim(roger) > roger[1:4, 1:4] > dim(roger.gnames) > roger.gnames[1:4, ] > roger.cl I got error messages. I opened the golub.RData file and it looks completely different to my "eset" or "roger" file. So this is the reason for the errors on running MULTTEST . I would appreciate instructions how do I make the *.RData file to run the multtest package. Many thanks in advance for the help. Roger Roger L. Vallejo, Ph.D. Assist. Professor of Genomics & Bioinformatics The Pennsylvania State University Department of Dairy & Animal Science 305 Henning Building University Park, PA 16802 Phone: (814) 865-1846 Fax: (814) 863-6042 Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> [[alternative HTML version deleted]]

You are making things difficult on yourself. All multtest wants is a matrix of data and a classlabel vector. The .RData file you use in the vignette is simply to make things easier to distribute. Do something like this: eset <- rma(Data) #Exactly equal to what you did, but I think it will be much faster teststat <- mt.teststat(exprs(eset), treat) # Here I am assuming that treat is a vector of 0's and 1's 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 >>> "Roger Vallejo" <rvallejo@psu.edu> 03/08/04 09:30AM >>> I would like to have an idea on my FDR and I thought that the MULTTEST package will do it. I read the MULTTEST.pdf manual and it is quite clear how to run the golub.RData example file. The problem is on how to run MULTTEST in my arrays data. To begin, how do I make the *.RData file using my data? Which of my files do I use? It seems that I have to use the output file after using this R function: > eset <- expresso(Data,bgcorrect.method="rma", normalize.method="quantiles", pmcorrect.method="pmonly", summary.method="medianpolish") I used then: > roger=exprs(eset) > roger.gnames=geneNames(eset) > roger.cl=treat > data(roger) > dim(roger) > roger[1:4, 1:4] > dim(roger.gnames) > roger.gnames[1:4, ] > roger.cl I got error messages. I opened the golub.RData file and it looks completely different to my "eset" or "roger" file. So this is the reason for the errors on running MULTTEST . I would appreciate instructions how do I make the *.RData file to run the multtest package. Many thanks in advance for the help. Roger Roger L. Vallejo, Ph.D. Assist. Professor of Genomics & Bioinformatics The Pennsylvania State University Department of Dairy & Animal Science 305 Henning Building University Park, PA 16802 Phone: (814) 865-1846 Fax: (814) 863-6042 Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor