This is a test version of Biostars. For the public version, visit https://www.biostars.org.
RNASeq deseq2

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?

deseq2 rnaseq
• 1,829 views • link
written by Rob • Rob

1 answer

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

• 0 views • link
written by kashiff007 kashiff007

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?

• 0 views • link
written by Rob • Rob

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.

• 0 views • link
written by kashiff007 kashiff007

thank you very much

• 0 views • link
written by Rob • Rob

Log in to answer this question.

More posts like this
  • CPTAC data, duplicate sample
    written by Rob • Rob
    Hi all, I am using DESeq2 package to normalize CPTAC data. However, I got error when reading my metadata: duplicate 'row.names' are not allowed So, …
  • RNA-seq data, normality test, stat test
    written by Rob • Rob
    Hi friends, Do you know how to do a normality test for RNA-seq data set with 60 columns of patients ( 3 groups of phenotypes) …
  • RNA Seq HTSeq download GDC portal
    written by Rob • Rob
    Hi friends, I am trying to download ht-seq file form GDC portal but it gives me one file for each patients. Can you please let …
  • RNA-Seq HTseq galaxy DE analysis
    written by Rob • Rob
    Hi friends I have htseq data from TCGA. it contains patients name in first row and genes in first column : 200 columns and 20000 …
  • differential expression- coding genes
    written by Rob • Rob
    hello friends, I performed differential expression analysis with DESeq2 package. my data is HT-seq count data and protein coding genes. in the result TUNAR gene …
  • HT-Seq count data
    written by Rob • Rob
    Hi friends How should I split my data of 500 patients with RNA seq data into 2/3 training and 1/3 validation sets randomly? I tried …
  • correlation matrix for HTSeq data
    written by Rob • Rob
    Hi friends I want to make a correlation matrix in R for HT-Seq data and a continuous variable (each patient has one value), to see …
  • Normality test for rna seq data
    written by Rob • Rob
    Hello friends I want to know how to test HT-Seq count data for normality in R? Any body has any idea? Thnx
  • TCGAbiolinks HT-Seq count
    written by Rob • Rob
    Hi friends I am trying to get HT-Seq count data with TCGAbiolinks in R. what I get is S4 data and I do not know …
  • Negative values HTSeq2
    written by Rob • Rob
    Hi friends I have HTSeq data that is Log2 (X+1), I revert them to original data in excel this way: X^2=y and then the y-1=original …