I am running DESeq on RNAseq data. I have two conditions, three replicates for each.
I would like to find the top 100 differentially expressed genes and look at them in a heat map.
I have done
estimateDispersions with the default settings and then did
nbinomTest on the resulting data. I have a list of genes with significant p-values I was thinking were my genes of interest. However, when I look at the DESeq vignette I see that to look at the data on the heatmap, they used
My question is, should I be running
nbinomTest with data from estimateDispersions method
blind or another option? Is it fair to use the default settings, choose my top 100 genes, and THEN get variance stabilized data and look at the genes in the heat map?
Thanks for any insight you may have.