I have one question regarding the approach of differential gene expression analysis from RNAseq data of cancer.
1) To find out the Defferentially Expressed Genes between low survived and high survived samples of patients. (example: here in my case, patients survived less than 1 year and patients survived more than 3 years)
I am using GDC data of lung cancer (TCGA-LUAD) and using this above approach i want to find the DEGs. So for this analysis i am using and following TCGAbiolinks package and its tutorials. but even if the TCGAbiolinks analysis is giving the DEG number but the heatmap of those genes is not showing any differentiating pattern. So i did the same analysis using edgeR analysis and limma using the expression set obtained from summarizedExperiment for the DEG, but then this analysis doesn't give any DEGs between less than 1 year and more than 3 years samples of patients.
SO my question is,
1) Is this approach of finding DEGs between less than 1 year and more than 3 years is correct? or is there anything i am missing in the analysis?
Suggestions regarding this approach will be very helpful and it will surly help me to clear my confusions. I look forward to hear valuable suggestions.
Thank you in advance.