Question: TCGA RNA-Seq data for gene correlation test
gravatar for JackieMe
7 months ago by
Wuhan University, Wuhan, China
JackieMe10 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 • 488 views
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