Hi all,

I was wondering what is the best way to quantitate transcriptional heterogeneity for each condition compared using DESeq2.

Not sure whether they are right, but was thinking of the following options:

1) Run DESeq2 on individual condition (design =~1) and compare medians for gene dispersion

2) Calculate the Shannon Index using the 'vegan' package for each gene in each given condition using the rlog matrix and compare medians

Any suggestion would be much appreciated!

Thanks

I like (1) to compute each condition's variability.