Question: Finding differentially expressed genes between samples from different studies
0
gravatar for majzoub.ruba
2.6 years ago by
majzoub.ruba0 wrote:

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?

ADD COMMENTlink written 2.6 years ago by majzoub.ruba0
3

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by WouterDeCoster37k

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.

ADD REPLYlink written 2.6 years ago by majzoub.ruba0
1

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.

ADD REPLYlink written 2.6 years ago by keith.hughitt250

Thank you very much keith.hughitt

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by majzoub.ruba0

Thank you very much WouterDeCoster.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by majzoub.ruba0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1149 users visited in the last hour