Question: Help interpreting error from DEXSeq
1
gravatar for squando
4 months ago by
squando10
squando10 wrote:

Hello all, I was wondering if anyone could help me with interpreting this error message I got when I tried to run DEXSeq. I prepared the GTF file and performed exon counts on my BAM files before inputting them into DEXSeq, and ended up with this:

Fatal error: An undefined error occured, please check your input carefully and contact your administrator.
    converting counts to integer mode
    Warning message:
    In DESeqDataSet(rse, design, ignoreRank = TRUE) :
      some variables in design formula are characters, converting to factors
    using supplied model matrix
    using supplied model matrix
    using supplied model matrix
    Error in getListElement(x, i, ...) : 
      GRanges objects don't support [[, as.list(), lapply(), or unlist() at
      the moment
    Calls: DEXSeqHTML ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
rna-seq dexseq • 220 views
ADD COMMENTlink modified 4 months ago by Lance30 • written 4 months ago by squando10

It looks like you input something in the wrong format. Please post the exact command that produced this and maybe a few before it for context.

ADD REPLYlink written 4 months ago by Devon Ryan88k

I've just run into the same error and haven't been able to track it down yet. BTW, the error I got was from running DEXSeq in Galaxy, though the error message is from the DEXSeq function DEXSeqHTML. Has anyone tracked anything down about this yet?

ADD REPLYlink written 4 months ago by Lance30

BTW, I have posted a message on the Bioconductor support site about this issue.

ADD REPLYlink written 4 months ago by Lance30
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