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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?

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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.

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  • $\begingroup$ thanks a lot nitesh $\endgroup$
    – user9114
    Oct 15, 2022 at 20:26
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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.

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  • $\begingroup$ thanks a lot, peter. Can I use edgeR removebatcheffect? $\endgroup$
    – user9114
    Oct 15, 2022 at 20:26
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    $\begingroup$ It should work as well. $\endgroup$
    – Peter Langfelder
    Oct 18, 2022 at 0:57
  • $\begingroup$ 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 $\endgroup$
    – user9114
    Oct 31, 2022 at 12:39

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