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  • DEXSeq error in fitDispersionFunction

    Hi to all
    I have a problem with running fitDispersionFunction in DEXSeq.
    I have 2 conditions, 3 replicates each.
    Every step from the DEXSeq manual so far went smoothly, but when I run the fitDispersionFunction (of course after running estimateDispersion) I get an error saying:

    Error in fitDispersionFunction(ecs):
    no CR dispersion estimations found, please first call estimateDispersions function.

    I thought it was because of the parallel processing issue as the manual says, since I tried to run it on 20 cores, but I get the same problem when running without nCores option.

    Can anyone help with solving this problem?
    Thanks!

    Ana Marija

  • #2
    You'll need to post the code you use (all of the relevant steps).

    Comment


    • #3
      Hi @unicornich,

      If you ar using R-3.0.*, have a look at this link,



      otherwise, could you include what @dpryan asked and the output off your sessionInfo()?
      Alejandro

      Comment


      • #4
        @areyes
        I work with R 3.0.3 and latest DEXSeq version.
        And your suggestion worked! It just takes a huge amount of time because I'm still getting errors with nCores option. But I can wait, what matters is it works!
        Thank you so much!

        @dpryan
        I followed basically the exact steps from the manual, but here they are anyway for future readers:
        Code:
        folder="/Volumes/Temp/Anna/counting/dexseq_counts"
        countfiles=dir(folder)
        countfiles=paste(folder,countfiles,sep="/")
        
        ecs=read.HTSeqCounts(countfiles=countfiles[c(7:9,10:12)],design=factor(c("T23","T23","T23","T29","T29","T29")),"/Volumes/Temp/Anna/counting/dmel-all-transcript-r5.49-oregonR-forDEXseq-notaggr.gff")
        ecs=estimateSizeFactors(ecs)
        ecs=estimateDispersions(ecs)
        ecs=fitDispersionFunction(ecs)
        ecs=testForDEU(ecs)
        ecs=estimatelog2FoldChanges(ecs)
        res1=DEUresultTable(ecs)

        Comment

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