Question

differentially expressed miRNA

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7.2 years ago

lilly ▴ 10

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 • 2.6k views

ADD COMMENT • link updated 7.2 years ago by Emilio Marmol ▴ 180 • written 7.2 years ago by lilly ▴ 10

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

ADD REPLY • link 7.2 years ago by Sparrow_kop ▴ 260

score 2 · Answer 1 · 2017-09-06

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7.2 years ago

Emilio Marmol ▴ 180

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.

ADD COMMENT • link 7.2 years ago by Emilio Marmol ▴ 180

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

ADD REPLY • link 7.2 years ago by lilly ▴ 10

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

ADD REPLY • link 7.2 years ago by Emilio Marmol ▴ 180