HI, I am trying to obtain transcript level expression using Aroma.affymetrix /FIRMA. I did following steps,
*Creating directories*: work directory: aromaaffy_test CDF dir: aromaaffy_test/annotationData/chipTypes/HuEx-1_0-st-v2/ Data dir: aromaaffy_test/rawData/GBM/HuEx-1_0-st-v2/ *CFD: * HuEx-1_0-st-v2.cdf (name changed; downloaded from HuEx-1_0-st-v2,coreR2,A20070914,EP.CDF <http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20070914,EP/HuEx-1_0-st-v2,coreR2,A20070914,EP.cdf> [38 MB] Core probesets: 18,708 units/transcript clusters, 284,258 groups/probesets, and 1,082,385 probes.) Data: *.CEL files R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) After setting work directory to aromaaffy_test/ Rcode: library(aroma.affymetrix) verbose <- Arguments$getVerbose(-8, timestamp=TRUE) cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2") cs <- AffymetrixCelSet$byName("GBM", cdf=cdf) setCdf(cs, cdf) bc <- RmaBackgroundCorrection(cs) csBC <- process(bc,verbose=verbose) qn <- QuantileNormalization(csBC, typesToUpdate="pm") csN <- process(qn, verbose=verbose) getCdf(csN) plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) fit(plmTr, verbose=verbose) cesTr <- getChipEffectSet(plmTr) trFit <- extractDataFrame(cesTr, units=NULL, addNames=TRUE) trFit.mat <- extractMatrix(cesTr, units=NULL, addNames=TRUE) fit(plmEx, verbose=verbose) cesEx <- getChipEffectSet(plmEx) exFit <- extractDataFrame(cesEx, units=NULL, addNames=TRUE) exFit.mat <- extractMatrix(cesEx, units=NULL, addNames=TRUE) firma <- FirmaModel(plmTr) fit(firma, verbose=verbose) fs <- getFirmaScores(firma) Error: Getting terminated at: fit(plmTr, verbose=verbose) Error Message: Error in readCel(getPathname(this), indices = idxs, readIntensities = FALSE, : Argument 'indices' is out of range [1,284622]. In addition: Warning message: In (ns == 0L) & (nchar(unitNames) == 0L) : longer object length is not a multiple of shorter object length I did the same error earlier, when i used extended CDF's HuEx-1_0-st-v2,extendedR3,A20071112,EP.cdf.gz Extended + Core probesets: 147,476 units/transcript clusters, 804,085 groups/probesets, and 3,095,094 probes) I have following two queries. Could you let me know where I am doing wrong? Also, is it possible to get the expression values of the isoforms, corresponding to ENSEMBL ID,( i.e. ENSTxxxxxxxxx format) using this package? Best regards Manoj -- -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
