Finding differentially expressed genes between samples from different studies

Question

[majzoub.ruba]

I want to find differentially expressed genes between samples from different datasets in GEO database (not between samples from the same dataset) by Babelomics’ tools or other free and easy to use tools?

[WouterDeCoster]

So you want to compare treatment A in experiment 1 with treatment B in experiment 2? That might give you invalid results, since you cannot determine whether the differential expression is due to a) the treatment or b) a batch effect between the two experiments.

[majzoub.ruba]

I mean: For example, I want to compare the expression profile of an embryonic stem cell from a study with the expression profile of an induced pluripotent stem cell from another study to find the differentially expressed genes between them.

[keith.hughitt]

Then WouterDeCoster is correct - experiment and cell type are confounded and you cannot reliably detect differences between them. This would only work if you had both cell types for both studies.

[majzoub.ruba]

Thank you very much keith.hughitt

[majzoub.ruba]

Thank you very much WouterDeCoster.