Combining microarray, RNA Seq, whole & exome sequencing

Question

[Bine]

Good morning,

I would love your opinion on the following. For a project I would like to combine as much samples with gene expression as possible (it is a bit tricky to find data for this particular topic). I am therefore aiming to combine RNA Seq, Microarray, whole genome and exome.

I will use batch correction.

What are the possible issues with combining gene expression of whole genome / exome / RNA Seq & Microarrays? Can it affect my results?

Thanks a lot!

[i.sudbery]

Whole Genome and Whole exome are not gene expression technologies. They query the sequence of the genome, not the amount to which each is expressed. After that, I recommend the same as @Asaf. Process the RNA-seq and the microarray separately. In fact process each RNAseq study and each microarray study separately (where you have more than one study of each type) and then combine the p-values using meta analysis techniques.

Answer 1

[Asaf]

The path I would choose is run the analysis with each technology separately and then combine the results with a meta-analysis. I would also call my favorite statistician.