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differentially expressed miRNA

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??

rna-seq
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updated by Emilio Marmol Emilio Marmol • written by lilly • lilly

R package called Rlaziness

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written by lessismore lessismore

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

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written by Sparrow_kop Sparrow_kop

1 answer

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.

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written by Emilio Marmol Emilio Marmol

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

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written by lilly • lilly

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

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written by Emilio Marmol Emilio Marmol

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