Question: differentially expressed miRNA
1
gravatar for lilly
2.3 years ago by
lilly10
lilly10 wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.3 years ago by v82masae140 • written 2.3 years ago by lilly10
1

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

ADD REPLYlink written 2.3 years ago by Sparrow_kop220
2
gravatar for v82masae
2.3 years ago by
v82masae140
v82masae140 wrote:

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 COMMENTlink written 2.3 years ago by v82masae140

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

ADD REPLYlink written 2.3 years ago by lilly10
1

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

ADD REPLYlink written 2.3 years ago by v82masae140
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