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!