Question: (Closed) deseq2 dispersion esimation fit type changed only when computing vst
gravatar for tonja.r
3.8 years ago by
United Kingdom
tonja.r40 wrote:

 I have following output of DESeq2 on the following functions. It seems that if changes the fitType for dispersion only when I compute variance stabilized values. Why doesn't it change the dispersion fitType when the function DESeq is called?

dds.1 = DESeqDataSetFromMatrix(countData=signal, colData=Design, design=~condition)
> dds <- DESeq(dds.1)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> vst = varianceStabilizingTransformation(dds.1)
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.

deseq2 • 790 views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by tonja.r40

Hello tonja.rand!

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ADD REPLYlink written 3.8 years ago by Michael Love25k
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