Question: How do I calculate DE genes from RSEM data?
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gravatar for snoopy84
22 months ago by
snoopy840
snoopy840 wrote:

Hey,

I downloaded the TCGA data "RNA_Seq_v2_expression_median.txt" from cBioPortal. The profile description is: Expression levels for 20532 genes in 1212 brca cases (RNA Seq V2 RSEM).

Can I use limma to calculate differentially expressed genes from RSEM data (after log2 (rsem+1) normalization)? If not, which is the best method to perform DE genes in this data set?

I usually work with microarray data and I am new to RNAseq.

Cheers all :)

limma rsem rna-seq tcga • 1.0k views
ADD COMMENTlink written 22 months ago by snoopy840
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