differential expression analysis

Question

[Edalat]

hello,

I have 9 experiments (human RNAseq data (control/treatment)),I did RNAseq analysis by CLC genomics,now I want to do differential expression between 2 condition(control/treatment) by R.I need DE for all treated vs all controls samples (I mean I do not want DE for each experiment separately). is there any R package?

Answer 1

[firatuyulur]

DESeq2 is what you are looking for. Here you can find both the vignette and the example R script. Also I havent used CLC genomics; do you have the count data? If not, use another R package see here to get your counts and use DESeq2 afterwards. As long as you arrange the condition part well, you can put as many samples you want

Answer 2

[natasha.sernova]

See this article, it may help.

https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

[WouterDeCoster]

Preferably refer to the newest version: https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf

In addition, this and this are helpful workflows.

[natasha.sernova]

Sure, but the article from 2016 considers old version, DESeq... When DESeq2 is from 2014, isn't it?