Question: (Closed) deseq2 dispersion esimation fit type changed only when computing vst
0
3.3 years ago by
tonja.r40
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 • 660 views
modified 3.3 years ago • written 3.3 years ago by tonja.r40

Hello tonja.rand!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!