Question: differentially expressed miRNA
0
gravatar for lilly
18 months ago by
lilly0
lilly0 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 • 916 views
ADD COMMENTlink modified 18 months ago by v82masae120 • written 18 months ago by lilly0

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 18 months ago by Sparrow_kop190
1
gravatar for v82masae
18 months ago by
v82masae120
v82masae120 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 18 months ago by v82masae120

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

ADD REPLYlink written 18 months ago by lilly0
1

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

ADD REPLYlink written 18 months ago by v82masae120
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