Do I have to separate my interest genes from my count matrix and then perform differential expression analysis for them?

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2.5 years ago

Azade ▴ 20

Hi all, I am trying to study the differential expression of my interest genes in colon cancer. First, I've downloaded the RNA-Seq raw counts from TCGA and have built the count matrix. Now I normalized the raw counts by DESeq2 and want to know what should I do in this step? Do I have to separate the interest genes from my count matrix and then perform differential expression analysis for them? or build a shortlist based on the logFC and adj. p-value and then separate my genes if they exist in that shortlist?? Thanks for any help

TCGA DEA RNA-Seq • 585 views

ADD COMMENT • link updated 2.5 years ago by GenoMax 142k • written 2.5 years ago by Azade ▴ 20

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You should always let the entire dataset guide the analysis.

RNA-SEQ where only a subset of genes is of interest

ADD REPLY • link 2.5 years ago by GenoMax 142k

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