I was doing QC analysis in aroma in R on HuEx chip but got an error while trying to plot NUSE. ylim contains NA.
I'm running R 2.10(32bit) on a windows 7(64bit). my command: library(aroma.affymetrix) verbose <- Arguments$getVerbose(-8, timestamp=TRUE) chipType <- "HuEx-1_0-st-v2" cdf <- AffymetrixCdfFile$byChipType(chipType) print(cdf) cs <- AffymetrixCelSet$byName("tissues", cdf=cdf) bc <- RmaBackgroundCorrection(cs) csBC <- process(bc,verbose=verbose) qn <- QuantileNormalization(csBC, typesToUpdate="pm") csN <- process(qn, verbose=verbose) plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) fit(plmTr, verbose=verbose) qamTr <- QualityAssessmentModel(plmTr) plotNuse(qamTr) plotRle(qamTr) <<End of command I was able to run the previous on U95A data and Plus 2 data. Also, in the past I was able to run that on HuEx data. The cdf file I'm using is binary and used multiples ones (HuEx-1_0- st- v2,core,A20071112,EP.cdf, HuEx-1_0-st- v2,control,A20071112,EP.cdf, HuEx-1_0-st- v2,extended,A20071112,EP.cdf etc offered on Elizabeth's Column http://groups.google.com/group/aroma-affymetrix/web/affymetrix-defined-transcript-clusters?pli=1 ) Could you please point me how to fix this problem? Thanks in advance -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to firstname.lastname@example.org To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en