Question: deseq2 dispersion esimation fit type changed only when computing vst
gravatar for tonja.r
2.0 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)
-- 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 2.0 years ago by Michael Love15k • written 2.0 years ago by tonja.r40
gravatar for Michael Love
2.0 years ago by
Michael Love15k
United States
Michael Love15k 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 2.0 years ago by Michael Love15k
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