Question: DEXSeq Error for Conditions
gravatar for jjrin
16 months ago by
jjrin10 wrote:


I am trying to run DEXSeq and I made all of the count files using your DEXSeq-Count which was successful. The factor I am comparing is "Condition" and factor level 1 is called "GFP" while factor level 2 is called "ICD". These are different variables of my condition. I entered in all of the correct data and I followed the example given on the DEXSeq galaxy page. I also prepared the annotation using DEXSeq-Count as well. However I get the same error every time I try to run the final step of DEXSeq on my conditions. Thank you for your help!

Here is the error message:

Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
  some variables in design formula are characters, converting to factors
using supplied model matrix
Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) : 
  all gene-wise dispersion estimates are within 2 orders of magnitude
  from the minimum value, and so the standard curve fitting techniques will not work.
  One can instead use the gene-wise estimates as final estimates:
  dds <- estimateDispersionsGeneEst(dds)
  dispersions(dds) <- mcols(dds)$dispGeneEst
  ...then continue with testing using nbinomWaldTest or nbinomLRT
Calls: estimateDispersions ... estimateDispersions -> .local -> estimateDispersionsFit
dexseq galaxy deseq2 • 555 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by jjrin10
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This is a content issue: the input data is not variable enough to use this tool in Galaxy. The issue comes up when the tool is used line-command.

A prior post at Biostars discusses the situation (in another usage-context, but the failure interpretation is the same):

As well as these posts at the Bioconductor site:

You can do a search on the error message to get more information about the cause of the data issue and what others have done as a remedy line-command (when possible). Note that many of these options/additional tools are not currently available in Galaxy, although you could expand the tool wrapper (and pull-request against the current wrapper repository to have the additions considered for addition to the repo/Tool Shed version) if you have programming resource.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 16 months ago by Jennifer Hillman Jackson25k
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