[Wolfgang Huber]

Hi guys,

So I'm wondering about DEseq and the old and new methods for accounting for variability. I see that the new methods uses the regression line as default variability for the gene, unless the variability is above that line, in which case it will use that. I'm thinking about using "sharing-mode=per gene estimate" because I have my 5 replicates. Will this method just use the variability of that gene (e.g. IL8) or will it use the variability of all genes at that abundance?

Hi Bill,

from the man page of 'estimateDispersions':
'gene-est-only' - No fitting or sharing, use only the empirical value. This method is preferable when the number of replicates is large and the empirical dispersion values are sufficiently reliable.

Hope this helps
Wolfgang