Question: TCGA RNA-Seq data for gene correlation test
gravatar for JackieMe
2.7 years ago by
Wuhan University, Wuhan, China
JackieMe30 wrote:

I am new to Bioinformatics and still learning. I downlaoded TCGA RNA-Seqv2 data from FireHose:

and exact gene count data. Using DESeq2 for DEG analysis and got about 1900+ genes with logFC>=2 and FDR <0.01, tumor vs normal samples. Now I want to check somes DE genes for pairwise correaltion.

Here are my question:

  1. Is it the data I used right for DEG analysis ?
  2. Using cor or cor.test for correlation test, which data should I use? For example, m is a matrix with 2 genes like:


          geneA    geneB
sample1      12      101
sample2      13      140
samplen      10      200

I am using cor(m[,1], m[,2]) to get the correlation R, but I don't think raw count data is a good choice as count data of different genes varies a lot and samples get far away from each other in a dotplot. I am think about using FPKM data from TCGA portal to do correlation test and draw dotplot. Am I wrong?

Any advice would be appreciated.

rna-seq tcga R • 1.7k views
ADD COMMENTlink written 2.7 years ago by JackieMe30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1208 users visited in the last hour