Answers.Body: <p>Yes, if the expression datasets are from the same platform, you can merge all the datasets for common genes among them. However, if they are from different platforms then some batch correction needs to be done before analysis. You can plot a PCA to check how much variability there is among datasets from different platforms and then decide whether batch correction is needed.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-15T20:26:24.630Z
Answers.Text: thanks a lot nitesh
Answers.UserDisplayName: user9114
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-15T03:38:36.037Z
Answers.LastActivityDate: 2022-10-15T03:38:36.037Z
Answers.UserDisplayName: Nitesh Shriwash
Answers.Body: <p>I would try to process all data sets in a similar way, then combine them and batch-correct, e.g., using ComBat or WGCNA's own empiricalBayesLM.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-15T20:26:03.610Z
Answers.Text: thanks a lot, peter. Can I use edgeR `removebatcheffect`?
Answers.UserDisplayName: user9114
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-18T00:57:34.820Z
Answers.Text: It should work as well.
Answers.UserDisplayName: Peter Langfelder
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-31T12:39:50.880Z
Answers.Text: Hi @Peter could you please help me with this `https://bioinformatics.stackexchange.com/questions/19922/how-to-find-closely-related-genes-for-a-specific-gene-from-wgcna-modules`
Answers.UserDisplayName: user9114
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-10-12T11:51:00.130Z
Answers.LastActivityDate: 2022-10-12T11:51:00.130Z
Answers.UserDisplayName: Peter Langfelder
Body: <p>I have 8 RNA-seq datasets and am interested in looking at genes co-expressed with a specific gene.</p>
  <p>Among 8 RNA-seq datasets, 6 have less than 20 samples. Rather than working on each dataset individually for WGCNA, do you think I can merge all datasets and use them for WGCNA?</p>
  
Tags: <r><rna-seq><wgcna>
Title: Is it possible to integrate multiple gene expression datasets and use it for WGCNA?
ThreadText: # Is it possible to integrate multiple gene expression datasets and use it for WGCNA?
  
  (Asked by: username_0 on 2022-10-12)
  
  I have 8 RNA-seq datasets and am interested in looking at genes co-expressed with a specific gene.
  
  Among 8 RNA-seq datasets, 6 have less than 20 samples. Rather than working on each dataset individually for WGCNA, do you think I can merge all datasets and use them for WGCNA?
  
  **Tags:** r, rna-seq, wgcna
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2022-10-15. Score: 2
  
  Yes, if the expression datasets are from the same platform, you can merge all the datasets for common genes among them. However, if they are from different platforms then some batch correction needs to be done before analysis. You can plot a PCA to check how much variability there is among datasets from different platforms and then decide whether batch correction is needed.
  
  > **Comments:**
  > **username_0**: thanks a lot username_1  
  
  ---
  
  ### Answer by username_2 on 2022-10-12. Score: 1
  
  I would try to process all data sets in a similar way, then combine them and batch-correct, e.g., using ComBat or WGCNA's own empiricalBayesLM.
  
  > **Comments:**
  > **username_0**: thanks a lot, username_2. Can I use edgeR `removebatcheffect`?  
  > **username_2**: It should work as well.  
  > **username_0**: Hi @username_2 could you please help me with this `https://bioinformatics.stackexchange.com/questions/19922/how-to-find-closely-related-genes-for-a-specific-gene-from-wgcna-modules`  
  
  ---
  
  