is someone know how to calculate up and down regulated

Question

[Learner]

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

Answer 1

[Michael]

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.

[Learner]

@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 .

[Michael]

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.