I've read a lot of posts about integrating microarray datasets but couldn't get my answer clearly for this specific scenario.
I have 4 GSE numbers of microarray datasets which have different platforms. Their biological groups are as follows:
- GSE1: TypeA, TypeB, TypeC, TypeD
- GSE2: TypeA, TypeE
- GSE3: TypeE, TypeF
- GSE4: TypeF, TypeG
As you can see each dataset has one biological group in common with next dataset. (there would be no way to distinguish batch effect from biological effect if there were no groups in common)
I can't analyse each dataset separately because for example i want to perform a differential expression analysis between TypeB and TypeF. So i need to merge all these datasets into one.
here are my questions:
- Is it possible to merge these datasets into one? (considering i want to perform a differential expression analysis (DEA))
- should i normalize them before merging ? if yes what normalization techniques should i use?
- How to merge them and remove batch effect? (for example if i want to use limma for DEA)
Any help would be greatly appreciated.
Thanks in advance