What file is suitable for differential expression analysis

Q&A
1

hi, I would like to perform differential expression analysis between cell line. for that I need raw count expression data. I wonder what file is suitable for this matter as I saw several different read count files
thank you very much!

2

Hi,

The expected counts should suffice if you intend to use algorithms such as Deseq2.

Thanks,
Simone

3

Hi, I am also trying to perform DGE Analysis. The expected counts file you mention is it this file? Data | DepMap Portal

4

@bgs_94 Correct. Please see the Q&A section in the data overview tab for details on how to map Profile IDs to ModelIDs if needed.

5

Thank you very much!