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:
- Is it the data I used right for DEG analysis ?
- 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.