Question: Differential Expressed Genes by FPKM expression matrix
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gravatar for morteza.kouhsar
11 months ago by
morteza.kouhsar0 wrote:

Hello everybody

I have a FPKM RNA-seq expression matrix. which R package is good to calculate differential expressed genes?

deg rna-seq fpkm R • 742 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by morteza.kouhsar0

You can use ballgown provided you have data in ballgown required format. edgeR and DEseq2 needs raw counts.

ADD REPLYlink modified 11 months ago • written 11 months ago by cpad01128.8k

How many replicates do you have?

ADD REPLYlink written 11 months ago by Vijay Lakhujani3.0k

The data contains 457 samples and about 43000 RNAs.

ADD REPLYlink written 11 months ago by morteza.kouhsar0
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