Hi, I have run the following code using many Affymetrix arrays with good luck, however, when I run it on HTHGU133A arrays using the following CDF file (http://brainarray.mbni.med.umich.edu/Brainarray/Database/ CustomCDF/11.0.1/entrezg.download/HTHGU133A_Hs_ENTREZG_11.0.1.zip) that I convert to binary using convertCdf in the affxparser package, the expression file that is generated only contains zeroes. Any advice?
Thank you. Jen library(aroma.affymetrix) verbose <- Arguments$getVerbose(-8) timestampOn(verbose) #specify chipType chipType <- "HTHGU133A" #specify directory in rawData name<-"Bild" cdf <- AffymetrixCdfFile$fromChipType(chipType, tags="Hs_ENTREZG,BINARY") cs <- AffymetrixCelSet$fromName(name,cdf=cdf) #Backgroud correction bc <- RmaBackgroundCorrection(cs, tag="Hs_ENTREZG,BINARY") csBC <- process(bc,verbose=verbose) #quantile normalization qn <- QuantileNormalization(csBC, typesToUpdate="pm") csN <- process(qn, verbose=verbose) #estimate the overall transcript plmTr <- RmaPlm(csN) #fit PLM to data -- could use plmEx if we wanted exon level data fit(plmTr, verbose=verbose) #calculate residuals from PLM fit rs <- calculateResiduals(plmTr, verbose=verbose) #to extract estimates (exon or transcript) cesTr <- getChipEffectSet(plmTr) trFit <- extractDataFrame(cesTr, units=NULL, addNames=TRUE) write.table(trFit,file=txt.file,sep="\t") --~--~---------~--~----~------------~-------~--~----~ 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 [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
