Question: is someone know how to calculate up and down regulated
0
gravatar for Learner
3.6 years ago by
Learner 200
Learner 200 wrote:

Hello,

I would like to know if anyone knows how to calculate up or down regulated genes like this paper http://rzlab.ucr.edu/281f_microarray/4562.pdf

ADD COMMENTlink modified 3.6 years ago by Michael Dondrup47k • written 3.6 years ago by Learner 200
1
gravatar for Michael Dondrup
3.6 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

The paper has a Materials and Methods section, check Identification of E2-regulated genes. I give it to you that it might not be totally clear how to implement it, but then you need to ask a more specific question. I think I wouldn't use this method nowadays, because it doesn't look standard.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Michael Dondrup47k
1

@Michael Dondrup I agree with you but they did not explain the method very well. Is there any review on the state of the art of selection up and down regulated genes ? I would like to know the structure of the data, the differences between packages, I remember some years ago DEseq used to have the analysis for data without replicate but DEseq2 (i don't know). I am wondering why DEseq works on only integer values but for example limma works fine with values having decimal etc .

ADD REPLYlink written 3.6 years ago by Learner 200

It depends on the data, the paper is on microarray data. For RNA-seq you can use DESeq2, edgeR or voom. Up- or down then just depends on the sign of the log fold change. If you do not have replicates, then there is no state of the art though.

ADD REPLYlink written 3.6 years ago by Michael Dondrup47k
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 2.3.0
Traffic: 2122 users visited in the last hour