Question: Manually feed DESeq with dispersions
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gravatar for ruhollah.mb
6 months ago by
ruhollah.mb0 wrote:

I am dealing with a very special problem: I have to perform DESeq on the count data that belong to a single gene (only ONE gene, i.e. the count data has one row & 100 columns). The dispersion value is already available for the gene. (Actually, the dispersions were calculated by DESeq over a master count data with 19k genes )

Question: How can I use DESeq on this special count data?! I have to somehow feed the DESeq with the already-known dispersion value, becauseDESeq cannot calculate dispersion when there's only one gene in the count data.

deseq2 • 179 views
ADD COMMENTlink modified 6 months ago by Michael Love25k • written 6 months ago by ruhollah.mb0
Answer: Manually feed DESeq with dispersions
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gravatar for Michael Love
6 months ago by
Michael Love25k
United States
Michael Love25k wrote:

You can just use dispersions(dds) <- ... to supply your own dispersion estimates rather than estimating them with DESeq2. Instead of running DESeq() you would run the individual steps, see ?DESeq.

ADD COMMENTlink written 6 months ago by Michael Love25k
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