Hi everyone, I am trying to use the read.dilution function of affycomp library, and I am getting the following error message: "Error in "[.data.frame"(d, , rownames(pData(dilution.phenodata))) : undefined columns selected" Looking at the code of the function I see that it is trying to select columns with names like: "94394hgu95v2a11" "94395hgu95v2a11" ... while the data frame d has columns with names like "94394hgu95a11" "94395hgu95a11"... . I could perhaps solve the problem by inserting the missing "v2" in the column names of the .csv file but I wonder if this is the right thing to do. Is possible that the 75 slides data set that I received form Genelogic with .cel files names like "94394hgu95a11" "94395hgu95a11"... is not the one read.dilution was conceived to deal with? Thanks for any suggestion, Laurentiu ---------------------------------------------- Dr. Laurentiu Adi Tarca Post Doc. in Bioinformatics Forest Biology Research Center C-E-Marchand Bld, 3113 Laval University Quebec, (Qc) G1K-7P4 Tel: (418) 656-2131 ext. 4509 Mobile: (418) 262-7125 e-mail: ltarca@rsvs.ulaval.ca www.gch.ulaval.ca/ltarca

genelogic has sent you the wrong files. but its a trivial problem. the cdf for these files should be the hgu95av2. and as you noted the names should be different. if you are using the affy package, and the dilution data is in a variable called "Data", to process the data you should do this: Data@cdfName <- "hgu95av2" before doing anyting else. On Mon, 30 Aug 2004, Tarca Adi Laurentiu wrote: > > > > Hi everyone, > I am trying to use the read.dilution function of affycomp library, and I am > getting the following error message: > > "Error in "[.data.frame"(d, , rownames(pData(dilution.phenodata))) : > undefined columns selected" > > Looking at the code of the function I see that it is trying to select > columns with names like: "94394hgu95v2a11" "94395hgu95v2a11" ... > while the data frame d has columns with names like "94394hgu95a11" > "94395hgu95a11"... . > I could perhaps solve the problem by inserting the missing "v2" in the > column names of the .csv file but I wonder if > this is the right thing to do. > Is possible that the 75 slides data set that I received form Genelogic with > .cel files names like > "94394hgu95a11" "94395hgu95a11"... is not the one read.dilution was > conceived to deal with? > > Thanks for any suggestion, > Laurentiu > > ---------------------------------------------- > Dr. Laurentiu Adi Tarca > Post Doc. in Bioinformatics > Forest Biology Research Center > C-E-Marchand Bld, 3113 > Laval University > Quebec, (Qc) > G1K-7P4 > Tel: (418) 656-2131 ext. 4509 > Mobile: (418) 262-7125 > e-mail: ltarca@rsvs.ulaval.ca > www.gch.ulaval.ca/ltarca > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >