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Question: DiffBind: How could I debug estimateDispersionsFit (required by DBA_DESEQ2)
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gravatar for zhaolin20042008
7 months ago by
zhaolin200420080 wrote:

Hi, 

I got an error when I used DiffBind to treat a human ATAC-seq library data set. (see  https://support.bioconductor.org/p/94915/).ATAC-seq is the data set like DNase-seq, the enrichment of open chromatin region are variable. 

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.
You can instead use the gene-wise estimates as final estimates:
dds <- estimateDispersionsGeneEst(dds)
dispersions(dds) <- mcols(dds)$dispGeneEst

I knew the reason but I failed to debug using trace () at DBA_DESEQ2 because it is not a function.Could anyone suggest a solution? Thanks a lot. 

ADD COMMENTlink written 7 months ago by zhaolin200420080
1

Hi,

If you want to debug estimateDispersionsFit you can debug it directly:

> debug(DESeq2::estimateDispersionsFit)

> x = dba.analyze(...)

Then use the debug commands to step through it, when R stops in that function.

ADD REPLYlink written 7 months ago by Gord Brown560
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