Question: DEXSeq Error for Conditions
gravatar for jjrin
4 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 • 152 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson23k • written 4 months ago by jjrin10
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson23k 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 4 months ago by Jennifer Hillman Jackson23k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 88 users visited in the last hour