I am trying to subset the samples according to condition type from a particular GSE from Gene Expression Omnibus (GEO). This particular GSE has data from two platforms:

 - Affymetrix Human Genome U133A Array
 - Affymetrix Human Genome U133B Array

I wanted to take samples from both these platforms and proceed with normalisation and deducing expression values for further WGCNA analyses.

My question is can we do the normalisation of samples from both these samples together or should I do it separately and later merge them (As the probe IDs of the two platforms will be different) ?

Thanking you in advance!


This has been done previously in 2 studies (possibly many more):

 - <a href="https://www.ncbi.nlm.nih.gov/pubmed/17699851">Secreted
   frizzled-related protein 1 loss contributes to tumor phenotype of
   clear cell renal cell carcinoma</a>
 - <a href="https://www.ncbi.nlm.nih.gov/pubmed/20502531">Pathway
   signature and cellular differentiation in clear cell renal cell
   carcinoma</a>

Both of these utilised this GEO dataset: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6344">GSE6344</a>

The methods that they used for merging, which involves the determination of a scaling factor on raw signal data, are here: ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE6nnn/GSE6344/suppl/GSE6344_MethodsDetails.PDF

This topic has also been discussed on both Biostars ( https://www.biostars.org/p/56657/ ) and Bioconductor a few times.

*[just briefing everyone]*

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**The key to your particular question is that you just want to run WGCNA on the data.** As WGCNA is fundamentally based on correlation, in this case, you just need to process each array experiment independently and then combine the final normalised datasets together. The merged dataset then becomes the input to WGCNA. Obviously only  combine the datasets where there are common genes.

An optional transformation for you is to normalise the arrays independently, covert the normalised expression values to the Z-scale, and then merge everything together.

If you want to start conducting statistical analyses other than WGCNA, then it's a different story and that particular topic is hot and provides for debate across the forums.

Kevin