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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?
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.
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.
removebatcheffect?
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https://bioinformatics.stackexchange.com/questions/19922/how-to-find-closely-related-genes-for-a-specific-gene-from-wgcna-modules
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