WGCNA of two different cohorts study
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suphamon.j • 0
Last seen 15 hours ago

Hi I would like to ask for suggestion how can I normalize the dataset before WGCNA analysis since I have two cohorts of my study. As you can see from the diagram; cohort 1 == start with 'S' and cohort 2 == start with 'RAW'. Hereby, I used log2(RPM+1) value for each sample as the input. However, the dendrogram shown that I have two batch of study (As originally these two set are from different cohorts study but I would like to analyze them together using WGCNA to distinguish which gene are related to 'P' trait.

my question is

  1. how can I normalize my log 2(RPM+1) between two cohort study?
  2. is there any batch correction method recommended to use before wgcna analysis. the dendrogram of sample of their log2(RPM+1) Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
Combat DESeq2 edgeR DifferentialExpression WGCNA • 43 views

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