Hello, I have a large dataset of ~10000 CEL files that needs to be normalized. I tried using aroma.affy for this, but the job is running for more than 3 weeks and in need of help/suggestions. The data is in standard affy rat2302 chip. I steps I used are (based on: http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis):
library("aroma.affymetrix") library(rat2302cdf) verbose <- Arguments$getVerbose(-8, timestamp=TRUE) chipType <- "rat2302" cdf <- AffymetrixCdfFile$byChipType(chipType) #, tags="r3") cs <- AffymetrixCelSet$byName("tissues", cdf=cdf) bc <- RmaBackgroundCorrection(cs) csBC <- process(bc,verbose=verbose) qn <- QuantileNormalization(csBC, typesToUpdate="pm") csN <- process(qn, verbose=verbose) plm <- RmaPlm(csN) fit(plm, verbose=verbose) All steps were ok but the last step : fit(plm,verbose=verbose) is running for nearly 3 weeks. Is this needed for probe summarization? What exactly does this fit do? Any suggestion will be helpful. Thanks, Rafi -- -- 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 firstname.lastname@example.org 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.