Hi everyone,

I'm currently analyzing a RNA-Seq data using DESeq2. Looking at the FAQ's in https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html, concerning the subset of data, the authors recommend "users to run samples from all groups together, and then use the contrast argument of the results function to extract comparisons of interest after fitting the model using DESeq."

However, they show an example of when to subset: when we have one group that has a within-group variable higher than the remaining groups. Thus, I would like to know if we can use `vegan::betadisper`

, a function to assess homogeneity of variances within-groups to determine if I should proceed or not with subsetting.

Thanks in advance!

Thanks for the feedback!

I got the idea from amplicon sequencing analysis, where they normally use PERMANOVA and, consequently, the

`betadisper`

functions.This could be a good addition to help users to know if the groups have similar variances, besides EDA.

Hi,

Do you export the counts from the DESeq2 object to use in the PERMANOVA analysis? If yes, what kind of numbers do you use, normalised, vst, other?

Jon

Hey,

I'd say you would use the distance matrix based on the results from rlog or vst functions, the same you would use to make the PCA.

Cheers,

André

Of course, I see. Thanks!