Body: <p>From this link <a href="https://support.bioconductor.org/p/67237/" rel="nofollow noreferrer">remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline</a>, I have learned that depending on context, it is perfectly valid to remove X and Y chromosomal genes in an RNA-seq dataset before doing differential expression analysis. However I only have access to the count matrix and not the <strong>bam</strong> files of the RNA seq data I am analysing. Is it advisable to do the X and Y chromosome gene removal at the level of the count matrix? I am talking about removing all rows that contain X and Y chromosomal genes from the <strong>.csv</strong> count matrix file read in to <strong>RStudio</strong> before proceeding to create the <strong>DESeq2</strong> object.</p>
  
  <p>Thank you in advance for your kind response.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-09T13:09:02.550Z
Comments.Text: First off, it can be valid, but why do you want to do so? In my lab we use them as a validation (does sample X that is a male, has gene expression of Y?). I think that removing them leads to more work with unclear benefit: what if there is a relevant gene in the X chromosome?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-10T11:59:55.047Z
Comments.Text: Why do you want to do this? It is almost never a good idea and will most likely not have the effect that you think it will (e.g., it won't remove gender differences).
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-11T12:04:15.600Z
Comments.Text: @Devon Ryan :  Thank you very much for your response. Do you please have a supporting publication?
Comments.UserDisplayName: Charles
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-11T12:08:09.717Z
Comments.Text: No one would ever bother writing a paper about something that is (A) almost never done and (B) rarely useful.
Comments.UserDisplayName: Devon Ryan
Tags: <rna-seq><deseq2>
Title: Is it advisable to remove X and Y chromosome genes in a bulk RNA-seq dataset at the level of the count matrix?
ThreadText: # Is it advisable to remove X and Y chromosome genes in a bulk RNA-seq dataset at the level of the count matrix?
  
  (Asked by: username_0 on 2019-04-09)
  
  From this link [remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline](https://support.bioconductor.org/p/67237/), I have learned that depending on context, it is perfectly valid to remove X and Y chromosomal genes in an RNA-seq dataset before doing differential expression analysis. However I only have access to the count matrix and not the **bam** files of the RNA seq data I am analysing. Is it advisable to do the X and Y chromosome gene removal at the level of the count matrix? I am talking about removing all rows that contain X and Y chromosomal genes from the **.csv** count matrix file read in to **RStudio** before proceeding to create the **DESeq2** object.
  
  Thank you in advance for your kind response.
  
  **Tags:** rna-seq, deseq2
  
  > **Comments:**
  > **username_1**: First off, it can be valid, but why do you want to do so? In my lab we use them as a validation (does sample X that is a male, has gene expression of Y?). I think that removing them leads to more work with unclear benefit: what if there is a relevant gene in the X chromosome?  
  > **username_2**: Why do you want to do this? It is almost never a good idea and will most likely not have the effect that you think it will (e.g., it won't remove gender differences).  
  > **username_0**: @username_2 :  Thank you very much for your response. Do you please have a supporting publication?  
  > **username_2**: No one would ever bother writing a paper about something that is (A) almost never done and (B) rarely useful.  
  
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  ## 0 answers
  
  