RNAseq data DEG analysis - DESeq2 normalized data

Question

[sushimoto]

Hello, this is my 3rd question in a week. Sorry about that.

1) So it seems like I have finally found data to do differentially expression analysis. So my question is, can I do DESeq2 differential expression analysis of the data from this link: https://xenabrowser.net/datapages/?dataset=TCGA-GTEx-TARGET-gene-exp-counts.deseq2-normalized.log2&host=https%3A%2F%2Ftoil.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.

2) If I can, should I skip the normalization?

3) If I cannot, in this link (https://xenabrowser.net/datapages/?cohort=TCGA%20TARGET%20GTEx&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443) which "gene expression RNAseq" dataset would be suitable for DEG analysis?

Thanks in advance.

Answer 1

[dsull]

1) You can't use because those data are already normalized and log-transformed.

3) RSEM expected_count is best to start off with for differential expression.

[sushimoto]

Thanks a lot!