Question: deseq2 dispersion esimation fit type changed only when computing vst
gravatar for tonja.r
22 months ago by
United Kingdom
tonja.r30 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)
-- 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.
ADD COMMENTlink modified 22 months ago by Michael Love14k • written 22 months ago by tonja.r30
gravatar for Michael Love
22 months ago by
Michael Love14k
United States
Michael Love14k wrote:
Briefly, because the estimation of dispersion using the "blind" design formula gives different estimates than using the formula in design(dds). See the manual page for the VST, the "blind" argument.
ADD COMMENTlink written 22 months ago by Michael Love14k
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