I'm working with with DESeq2 to make a DE analysis between samples in two different conditions . After differential expression analysis I'm interested to perform two further steps:
1) I want to plot a heatmap showing the expression of the differential expressed genes in the different samples analyzed.
2) I'm interested to check a potential correlation (Spearman correlation) between DE genes expression and a specific variable.
Which type of normalization is suggested for these two type of analyzes?
I'm currently using
vst() normalization function to perform the correlation test (
cor.test() function) while using the normalized matrix retrieved with
counts(dds, normalized=TRUE) to better highlight the expression differences inside the heatmap. Is my approach correct?
Thanks for the help.