RNASeq deseq2

Question

[Rob]

Hi friends

I have RNASeq data fromTCGA as HT-seq format. I want to do Deseq2. some patient names are duplicated and deseq2 dose not accept them. How would I deal with the duplicated patients?

Answer 1

[kashiff007]

Rename the patient names with versions. Like P.1, P.2 and so on

[Rob]

Thanks So, you mean I should not remove any sample? this way for some patients, I will have more than one sample (with different count values=different counts for one person!!!) and for the rest just one sample. is it fine?

[kashiff007]

As you mentioned in your question, "some patient names are duplicated," which means they are different individuals, but they are named the same. So just change the name by adding a version at the end. And I think it should work.

[Rob]

thank you very much