Hi. On Tue, Jun 24, 2014 at 8:45 AM, <rafi...@gmail.com> wrote: > 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.
My first concern (more on this below): The formal Affymetrix name of this *chip type* is not 'rat2302', but rather 'Rat230_2' [http://aroma-project.org/chipTypes/Rat230_2]. It is very very ... very important that you understand the difference between *chip type* and *CDF*. If not, please spend a minute reading http://aroma-project.org/definitions/chipTypesAndCDFs > I steps I used are (based on: > http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis): > > library("aroma.affymetrix") > library(rat2302cdf) The Bioconductor package 'rat2302cdf' is *not* need by aroma.affymetrix, nor used. You can skip loading it. > > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > chipType <- "rat2302" > cdf <- AffymetrixCdfFile$byChipType(chipType) #, tags="r3") Since you're using chip type 'rat2302' here I wonder where you got the rat2302.CDF file from? It should have been named 'Rat230_2' if you got it from Affymetrix. Continuing, assuming that you got a hold of a proper Rat230_2 CDF file and renamed it to 'rat2302' (not correct, but will work). > 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? Yes, probe summarization is definitely needed and is a fundamental concept/step in almost all Affymetrix microarray analyses. Google 'Affymetrix probe summarization' or 'Affymetrix RMA' and you should gets heaps of references. > > Any suggestion will be helpful. Have a look here: http://aroma-project.org/howtos/ImproveProcessingTime Despite the title, the following thread should also be informative and helpful for speeding up probe summarization: aroma.affymetrix, Speeding up RmaBackgroundCorrection, started 2014-02-16 https://groups.google.com/forum/#!msg/aroma-affymetrix/U2MGe9778JI/IyzXk0GJnZQJ See my reply on March 7. Hope this helps Henrik > > 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 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. -- -- 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.
