Question: DEXSeq Error for Conditions
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jjrin • 10 wrote:
Hello,
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
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modified 16 months ago
by
Jennifer Hillman Jackson ♦ 25k
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written
16 months ago by
jjrin • 10
