Dear Dr. Love Michael Love and community,

I have one doubt regarding the "contrast" function in DESeq2. I have already followed the solved threads but I just want to make sure that I am thinking in the right direction.

In order to make a comparison between "control" and "stressed" genotypes, I am using the following code:

contrast=c("conditions","control","stressed")

I want to know the direction of comparison. I am assuming that If logFC < 0 then "control" is down-regulated and if logFC > 0, then "control" is up-regulated and vice-versa. Am I analyzing it in the right direction?

Thank you for your time.

Best regards,

Chanderkant

It seems like you might benefit from reading through the workflow:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html

See the part:

As res is a DataFrame object, it carries metadata with information on the meaning of the columns:...