Question: deseq2 dispersion esimation fit type changed only when computing vst
2.5 years ago by
tonja.r • 40
tonja.r • 40 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.
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