Hi Diego, I had a look at the data that you sent me. The problem indeed is that there are some probes listed in the probeAnno object that do not correspond to any features/probes of the ExpressionSet. > table(ProbeAnno["1.index"] %in% featureNames(eSet)) # all TRUE > table(ProbeAnno["10.index"] %in% featureNames(eSet)) # all TRUE > table(ProbeAnno["11.index"] %in% featureNames(eSet)) # 20 FALSE FALSE TRUE 20 16294 > ProbeAnno["11.index"][!(ProbeAnno["11.index"] %in% featureNames(eSet))] [1] "chr11.118393537.118393597" "chr11.118393665.118393725" [3] "chr11.118393916.118393976" "chr11.118393984.118394044" .... # lines removed [19] "chr11.118394982.118395042" "chr11.118395017.118395077" These are the chromosome-11 probes which do not appear in your ExpressionSet 'eSet'. Some of the other chromosomes also contain a couple of probes that are not contained in eSet. Therefore, your probeAnno object does not exactly correspond to your supplied ExpressionSet. In the development version of Ringo (v1.9.9), I have now added additional code which reports a warning in such a case and ignores non-corresponding probes from the probeAnno object. You will be able to obtain this development version in a few days from: http://www.bioconductor.org/packages/devel/bioc/html/Ringo.html For now, you should consider rebuilding your probeAnno object such that it matches the ExpressionSet eSet. For instance, you can remove all probes that are not in the featureNames(eSet) from the POS-data.frame/file before building the probeAnno object via 'posToProbeAnno'. Regards, Joern On Mon, 31 Aug 2009 16:33:28 +0000, Diego Villar wrote > Dear Joern, > > I looked at the output of the commands you suggested (in some instances > only a fragment of the output is copied): > > table(ProbeAnno["11.unique"]) > > 0 > 16314 > > table(ProbeAnno["11.index"]) > > chr11.990402.990462 chr11.990469.990529 > chr11.990589.990649 > 1 1 > 1 chr11.990598.990658 chr11.99098574.99098634 chr11.99098696.99098756 > 1 1 > 1 > Checking on the error as you indicated I retrieve the following values: > > smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno, > + modColumn = "Cy5", winHalfSize = 400) > > Chromosome 1 ... > 170809ds ... 261108no ... > Chromosome 10 ... > 170809ds ... 261108no ... > Chromosome 11 ... > 170809ds ... Error en newExprs[chridx, i] <- chrrm : > NAs no son permitidos en asignaciones subscritas > > Enter a frame number, or 0 to exit > > 1: computeRunningMedians(eSet, probeAnno = ProbeAnno, modColumn = > "Cy5", winHa > > Selecci?n: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> str(chridx) > int [1:16314] 40027 121370 99412 63143 131069 125479 54552 32661 81358 > 80190 ... > Browse[1]> str(i) > int 1 > Browse[1]> str(chrrm) > Named num [1:16314] NA NA NA NA 0.164 ... > - attr(*, "names")= chr [1:16314] "186594" "186802" "186874" > "186940" ... > > Thanks, > > Diego --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246926