Difficlty to find DEG between stages of umor from LUAD data

[Ankita Lawarde]

Hello
I am interested in TCGA analysis. I would like to see the differences in my gene of interest in multiple groups of lung cancer patients. DO you guys think I should use scaled_estimate or raw_count?
Thank you for your help

Hi,
I see you have worked on LUAD data from TCGA. I'm working on the LUAD data from Firehose and i want to find the DEG between tumor stages I and IV. but i don't know how to work with the RSEM normalized data.If you have worked on the same data and you know what processes needs to be done for this type of data please guide me. What R packages or what Statistical analysis should Be done to find the DEG between selected samples using R programming?

Your suggestions would really help me in this. I look forward to hear from you,

Thanks,
Ankita