Question: Differential expression analyses
0
gravatar for simaomc.bio
7 weeks ago by
Brazil
simaomc.bio0 wrote:

Hi!

I hope someone can help me with my problem.

My project aims to test the hypothesis that differentially expressed genes between germline tissues (ovaries and testes) may be at the origin of hybrid sterility that in most cases is only present in the male offspring. However, I don't know the best way to normalize different types of tissues (Do you know if I can use DESeq2 or do I need to use another one?)

If somebody can guide me in this matter I would be very grateful!

normalization deseq2 • 74 views
ADD COMMENTlink modified 6 weeks ago by Michael Love26k • written 7 weeks ago by simaomc.bio0
Answer: Differential expression analyses
0
gravatar for Michael Love
6 weeks ago by
Michael Love26k
United States
Michael Love26k wrote:

What are you samples? Can you describe them in more detail please?

ADD COMMENTlink written 6 weeks ago by Michael Love26k

We have performed RNA total sequencing in ovaries and testes of fruit flies, in two biological replicates. I have aligned the transcripts into the reference genome and now I need to perform the differential expression analyses between these tissues. But, the problem is the high number of male-biased genes in testes. So, I would like to know if DESeq2 is a good tool to perform this kind of analyses or if I should use another method to analyzed these data.

Thanks.

ADD REPLYlink written 6 weeks ago by simaomc.bio0

If you want to specify a set of control genes to use for normalization you can use controlGenes in estimateSizeFactors.

e.g.

dds <- estimateSizeFactors(dds, controlGenes=...)
dds <- DESeq(dds)

See ?estimateSizeFactors for more details.

ADD REPLYlink written 6 weeks ago by Michael Love26k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 378 users visited in the last hour