differentially expressed miRNA

Question

[lilly]

Hi I have downloaded miRNA seq from TCGA data. I have got many files such as raw counts, RPM and RPKM log2, if i want to find the differentially expressed genes, which data should i used and which R packages??

[Sparrow_kop]

Hi, you can try DESeq2 or edgeR which based on count values. They are the mainstreaming tools currently to do DE analysis.

Answer 1

[Emilio Marmol]

I would suggest doing differential expression analysis with bioconductor R packages like EdgeR, DESeq2, limma or NOISeq from raw counts, assuming those are the output of a kind of software tool like htseq-count of FeatureCounts or somewhat similar.

[lilly]

Thanks for the reply. One more question raw counts and read counts are same?

[Emilio Marmol]

Yes, well raw counts I refered as non previously filtered read counts. Raw read counts better said.