Answers.Body: <p>I think your question has been answered very well here:
  <a href="https://www.biostars.org/p/284775/" rel="nofollow noreferrer">https://www.biostars.org/p/284775/</a></p>
  <p>If you want to go deeper perhaps you can look at this paper by Li et al.
  <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4" rel="nofollow noreferrer">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4</a>
  where they argue that for large scale datasets (multiple conditions) both of these methods are not optimal and instead suggests using Wilcoxon rank-sum test to decrease chances of FDRs.</p>
  <p>Best,</p>
  <p>av</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-09T15:29:33.973Z
Answers.Text: i need to do proximal vs distal comparison, for that i need to convert my csv file it contains single gene id data multiple time i need to narrow it down to one how can i do that
Answers.UserDisplayName: noor fatimah
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-11-02T19:52:30.997Z
Answers.LastActivityDate: 2022-11-02T19:52:30.997Z
Answers.UserDisplayName: Avamys
Body: <p>I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data.</p>
  <p>However, I am struggling to understand their specific purpose, differences between them and underlying theory. The information is required for a thesis with an imminent deadline</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-29T15:11:52.160Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-10-30T11:08:49.043Z
Comments.Text: Hi @noor-fatimah, your question seems quite broad and not tied to a specific problem; are you able to make your question more specific, or give some more information on what you've already found out? Have you, for example, read the user's guides for [EdgeR](http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) and [DESeq2](http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)?
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-09T15:27:59.070Z
Comments.Text: i need to do proximal vs distal comparison, for that i need to convert my csv file it contains single gene id data multiple time i need to narrow it down to one how can i do that
Comments.UserDisplayName: noor fatimah
Tags: <deseq2><edger><homework>
Title: DESeq2 and EdgeR
ThreadText: # DESeq2 and EdgeR
  
  (Asked by: username_0 on 2022-10-29)
  
  I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data.
  
  However, I am struggling to understand their specific purpose, differences between them and underlying theory. The information is required for a thesis with an imminent deadline
  
  **Tags:** deseq2, edger, homework
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Hi @username_0-username_0, your question seems quite broad and not tied to a specific problem; are you able to make your question more specific, or give some more information on what you've already found out? Have you, for example, read the user's guides for [EdgeR](http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf) and [DESeq2](http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)?  
  > **username_0**: i need to do proximal vs distal comparison, for that i need to convert my csv file it contains single gene id data multiple time i need to narrow it down to one how can i do that  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-11-02. Score: 2 | Accepted answer
  
  I think your question has been answered very well here:
  <https://www.biostars.org/p/284775/>
  
  If you want to go deeper perhaps you can look at this paper by Li et al.
  <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02648-4>
  where they argue that for large scale datasets (multiple conditions) both of these methods are not optimal and instead suggests using Wilcoxon rank-sum test to decrease chances of FDRs.
  
  Best,
  
  av
  
  > **Comments:**
  > **username_0**: i need to do proximal vs distal comparison, for that i need to convert my csv file it contains single gene id data multiple time i need to narrow it down to one how can i do that  
  
  ---
  
  