Hi, I seem to get nothing but problems... I have the appropriate probe package but now when I try to run gcrma I get the error detailed below. I did a search and the only similar thing I found listed was with the Li-wong function where it was proposed that it might have something to do with the fact that some probesets had only 1 probepair. I've looked at the ATH array and there are some sets with only 8, 9 or 10 probesets. It does not seem to be a problem of masks on the CEL files as I've tried it with mulitple CELs from different sources (they are all several months old - did I hear something about a new binary format?). It must have something to do specifically with the gcrma method as rma(data) works fine. Any ideas how to overcome this problem, or other people with success on ATH1 arrays. I'm using R 1.9devel and latest BioC and gcrma (1.0.2) on win2k 2Ghz, 1GB RAM. Thanks Matt > data <- ReadAffy() > esetgcrma <- gcrma(data) Computing affinities Attaching package 'matchprobes': The following object(s) are masked from package:Biobase : combine ...Done. Adjusting for optical effect..........Done. Adjusting for non-specific binding.Error in quantile.default(y, Q) : Missing values and NaN's not allowed if `na.rm' is FALSE

HI, there seems to be a disagreement on how many pm probes there are on the chip. This is causing problem in matching the pm intensities with sequences. I am not sure if this is true for all ATH1 chip... After reading in your Cel file into "object", ########### pmIndex <- unlist(indexProbes(object,"pm")) length(pmIndex) #[1]251078 #however the probe package gives 251121 pm probe sequences. length(get("ath1121501probe")$sequence) [1] 251121 right now I am not sure which should be fixed-- whether the probe package has some redundent sequences that are not PM probes or the indexProbes missed some pm probes? Jean On Wed, 11 Feb 2004, Matthew Hannah wrote: > Hi, > > I seem to get nothing but problems... I have the appropriate probe package > but now when I try to run gcrma I get the error detailed below. > > I did a search and the only similar thing I found listed was with the Li-wong > function where it was proposed that it might have something to do with the > fact that some probesets had only 1 probepair. I've looked at the ATH array and > there are some sets with only 8, 9 or 10 probesets. It does not seem to be a > problem of masks on the CEL files as I've tried it with mulitple CELs from > different sources (they are all several months old - did I hear something > about a new binary format?). > > It must have something to do specifically with the gcrma method as rma(data) > works fine. Any ideas how to overcome this problem, or other people with > success on ATH1 arrays. I'm using R 1.9devel and latest BioC and gcrma (1.0.2) > on win2k 2Ghz, 1GB RAM. > > Thanks > Matt > > > data <- ReadAffy() > > esetgcrma <- gcrma(data) > Computing affinities > Attaching package 'matchprobes': > > > The following object(s) are masked from package:Biobase : > > combine > > ...Done. > Adjusting for optical effect..........Done. > Adjusting for non-specific binding.Error in quantile.default(y, Q) : Missing > values and NaN's not allowed if `na.rm' is FALSE > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >