Which normalization method do you prefer??

[Sora Yoon]

among RPKM, DESeq, TMM and so on...

Which one do you prefer and why??!

[dpryan]

Generally DESeq'2 method or TMM, depending on whether I'm using DESeq2 or edgeR (why? Because they're done by default and work fine). RPKM should never be used (there are many papers on this). Quantile normalization is also popular, though you wouldn't normally use that on count data (though you could use it in conjunction with limma). Generally you get the same results regardless of the method (except RPKM, which you should never use as a normalization method).

[Sora Yoon]

Thank you, Devon Ryan. I usually use DESeq but I just saw a company provided their client RNA-seq data normalized by RPKM.

[ithersam]

Please can someone solve this assignment by using Gauss elimination method (please write the procedure step by step so I could understand it). Thank you very much.
Update: if it is easy why wouldn't you do it?

[dpryan]

@ithersam: I hope you realize that we have absolutely no clue what you're talking about. BTW, you should do your own assignments.