Suppose if I have to collect the microarray gene datasets from GEO, is it necessary that I have to collect only diseased and normal samples? For example, breast cancer has various subtypes, if I got two different subtypes from one GEO datasets and another subtypes and normal from other GEO datasets, how will I combine and get the DEG?
I think a good rule of thumb is to download the control data with the diseased data from the same GEO. That is to say, you cannot use microarray from one submission, and analyse it with control/non-diseased data from a different submission, as it'll be from a different experiment.
Not sure specifically what type of data analysis you are trying to perform on the GEO data, but iPathwayGuide has the ability to take the output from GEO2R and provide a number of analyses including predicted miRNA analysis, GO analysis, Pathway analysis, and much more. It's super fast and super easy!
Here's a short video describing how to use the GEO2R and upload it into iPathwayGuide:
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That heavily depends from which question you are asking. What's the initial reason why you are downloading GEO datasets? Is that to check different subtypes or just to get an idea of DEGs in normal vs tumor samples?
Also, are those the same platforms? Are those different platforms? If you want to combine/compare different arrays you need to keep this in mind too. Are you downloading just the DEGs or the raw file to analyze? (wink wink this might be better)