<p>I&#39;d like to get my hands on a microarray dataset with as many conditions as possible. One thought that I had was to simply concatenate many individual microarray datasets together, however it seems that they often dont have the same probes, and sometimes are in different units (fold change, intensity, etc).</p>

<p>Is there a way I can download all the datasets of GEO, but only include datasets that have the same probes, and are normalized in the same way?</p>

Did you have a look at the <a href="https://www.ebi.ac.uk/gxa/home" target="_blank">Expression Atlas</a>? It integrates many gene expression experiments to make them comparable.