How to compare across Microarray datasets for a gene in Mice?

Question

How does one go about comparing expression levels of one gene across multiple microarray datasets pulled from different experiments/papers in mice? In my example, I've downloaded the expression levels for my gene of interest from different microarray datasets for different cell populations of interest (specifically healthy hematopoietic cells). How would I pool the datasets together?

Say I have common cell types from multiple datasets such as B-cells, would I be able to just combine them into one data frame and visualize them as one or would I need to normalize some aspect of that?

I'm really confused because I've had different people tell me different things.

Answer 1

If you are after expression of tissue-specific, but otherwise healthy wild-type mice, Bgee is really a great resource for you. They pull a lot of data, curate it and sort it in a single database that easy to browse. They also have lots of tools for comparative genomics (if you would be wondering about expression of an ortholog in a different species).

If you are just after the methodology of pulling expression data together from multiple sources be because you are interested in pulling data from specific papers, you can check their paper about the database. The pipeline is available on GitHub too.