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DESeq2 sharingMode and fitType

Hi, all! When I used DESeq2 to analyse the different expression genes, I was confused about two parameters of estimateDispersions, that is sharingMode and fitType.

The DESeq used 'sharingMode="fit-only",fitType="local"' as the default, however the DESeq2 set 'sharingMode="maximum",fitType="parametric"' as the default.

How could I select these two parameters? Could I change the default, like 'sharingMode="fit-only",fitType="parametric"'? My data had 10 samples and every sample only repeat twice, which is the best?

Thank you again and look forward to your feedbackssoon.

rna-seq
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written by hellosky2008 • hellosky2008

As a rule of thumb, go with default parameters of all tools unless you have a reason not to.

Can you use "fit-only"? Yes, but why do you think that's a good idea?

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written by Devon Ryan Devon Ryan

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