Hi Wolfgang, I downloaded the most recent version of arrayQualityMetrics and everything is working fine now. Thanks for writing this very helpful package. Matthew On 12/6/2011 5:24 PM, Wolfgang Huber wrote: > Dear Matthew > > Thank you for the report. It is difficult to say what is going on > without more details. In general, please always make sure you are > using the latest versions of Bioconductor, and include the output of > sessionInfo(). > > Beyond that, in order to diagnose/fix your problem, we would need an R > script that reproduces the error, and the necessary CEL files (maybe > one or two already suffice?) or the AffyBatch object. > > Best wishes > Wolfgang > > > On 12/6/11 10:59 PM, Matthew McCormack wrote: >> I get the following error when I run arrayQualityMetircs on an affybatch >> file that has 13 Affymetrix CEL files: >> Error in .local(object, ...) : subscript out of bounds >> >> The full command is: >> arrayQualityMetrics(expressionset = abatch, outdir = >> "AQM_GT_Jos5236-5248_Dec_11", force = TRUE, do.logtransform = TRUE) >> >> I also get the following error when running Harshlight on the same affy >> batch file: >> Error in indices2xy(i, nr = object at nrow) : >> Indices must start at 0 or 1 (please refer to the help file) ! >> >> I thought I would add the Harshlight error, because I'll bet the two are >> related. I did not generate the .CEL files. I received them and put them >> into an affy batch file with the command >> abatch <- ReadAffy() >> >> Any ideas as to what the problem is ? >> >> Matthew >> >> >> The information in this e-mail is intended only for t...{{dropped:21}}