Thank you very much！
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how to find differential genes using TCGA RPKM data
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!
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Please see the answer and comments to this post on Biostars: How to work with Level 3 data (RPKM values) from TCGA database
when I use the raw counts data to find differantial genes using DEseq2,should I remove the genes whose counts are 0?
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sunqiangzai •
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.
Thanks a lot @alolex
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