DEXSeq HTML report Error
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@aleksandarbaburskig-23324
Last seen 3.2 years ago

Hi, I have problem creating DEXSeq HTML Report (DEXSeq 1.34.0). Before this step everything works fine. But when I run:

   DEXSeqHTML(object = dxr1, 
                            FDR=0.05,
                            fitExpToVar = "condition",
                            path = "./",
                            file = "report.html",
                            BPPARAM = MulticoreParam(workers = 8))

analysis fails with following error:

Error: BiocParallel errors
element index: 44, 45, 46, 47, 48, 49, ...
 first error: 'relevel' only for (unordered) factors
 In addition: Warning message:
 stop worker failed:
   attempt to select less than one element in OneIndex 
 Execution haltedanalysis

or when I remove parallelisation, I get this error message:

Error in relevel.default(mf$exon, "others") : 
   'relevel' only for (unordered) factors
 Calls: DEXSeqHTML ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>

Sometimes it works for low number of files, but with more than 8 analysis always fails. Can someone help please :)

Aleksandar

DEXSeq • 859 views
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Entering edit mode

Thanks for reporting this. It is a bug resulting from the change on the R base defaults in stringsAsFactors=. I will fix this as soon as I find some time and let you know.

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Thanks a lot :) Aleksandar

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