how to find differential genes using TCGA RPKM data

Question

[sunqiangzai]

Hi there,I download some TCGA data from the website,now I want to find some differential genes between the normal and tumor groups.which package should be used to find the genes,and which datatype should I use,the RPKM data or the RAW counts? thank you!

Answer 1

[alolex]

Please see the answer and comments to this post on Biostars: How to work with Level 3 data (RPKM values) from TCGA database

[sunqiangzai]

Thank you very much！

[sunqiangzai]

when I use the raw counts data to find differantial genes using DEseq2,should I remove the genes whose counts are 0?

[alolex]

This is commonly done, however DESeq2 does this by default. I would recommend that you follow the vignette for DESeq2 and check out this tutorial in section 12.2, which explains the options for the independent filtering that you are referring to.

[sunqiangzai]

Thanks a lot @alolex