This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Considering that the basal expression level is not 0 for the calculation of the differential expression

Hello,

I am doing a RNA-Seq DE analysis with DESeq2 and I was told to not consider the gene basal expression level as 0, so, how would I do that step? Are they referring to the relevel function in DESeq2? or setting the control samples as the targets of the comparison? Or is there more to it that i am not aware of?

Also, would results differ a lot if I do the analysis as indicated in the DESeq2 tutorial and not do the "not considering basal expression level as 0" step ?

Thank you

deseq2 rna-seq differential-gene-expression
• 1,728 views • link
updated by Ram Ram • written by Pin.Bioinf Pin.Bioinf

I think this has to do with calculating fold changes and log changes. With basal levels of 0, you would end up dividing my zero and/or taking logs of 0s, both of which will give you infinite values.

• 0 views • link
written by Joe Joe

and I was told to not consider the gene basal expression level as 0

Who told you?

Are you referring to zero raw counts or 0 normalised counts?

• 0 views • link
written by Kevin Blighe Kevin Blighe

My biologist fellow. Normalized counts

• 0 views • link
written by Pin.Bioinf Pin.Bioinf

You should obtain the logged counts and then covert these to the Z scale. Then work on expressed / not expressed based on the Z scores.

• 0 views • link
written by Kevin Blighe Kevin Blighe

Logged counts? You mean the log2 of my normalized data and then transform to Z scale?

• 0 views • link
written by Pin.Bioinf Pin.Bioinf

0 answers

No answers yet.

Log in to answer this question.

More posts like this