Question: RNA-Seq: Normalization to control conditions for DESeq
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gravatar for rachelpjlai
4.7 years ago by
rachelpjlai0 wrote:

Hi! I am still learning my RNA-Seq analysis and would greatly appreciate some help here.

Our study is to investigate the pathways associated to interferon-gamma (IFNg)-induced control of infection with bacteriaX. There are four experimental groups (done as 3 biological replicates):

1) Uninfected without IFNg
2) Uninfected with IFNg
3) BacteriaX infected without IFNg
4) BacteriaX infected with IFNg

I aligned the data to the hg19 reference genome using TopHat2 followed by HTSeq Count. My question is on the DESeq2 part: what we are really interested is the transcriptional changes associated to both infection and the presence of IFNg.

Is it possible to normalize condition 3 to condition 1 and condition 4 to condition 2, before performing DESeq2?

Or are there more approporiate ways to analyze the data?

Any suggestions will be greatly appreciated! Many thanks in advance!

ADD COMMENTlink written 4.7 years ago by rachelpjlai0
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