Hello! So, I have fifteen GEO datasets to analyze. All of them are very similar (studies with microRNAs related to the same disease/same type of samples/all measured with RNA-seq platforms, microarrays were excluded).
I want to investigate microRNAs related to a specific signaling pathway in the disease. The comparison group consists of mild vs. controls, and initially I want to use all GEO data. At first, I'm thinking of analyzing all GEO data together (so I can optimize my time) to find DEGs related to the conditions. It was possible to download the series matrix (.txt.gz format) for all of them, as I did. But I don't know how to make a pipeline to reprocess all these data from scratch, because I think that's the only option, right? I mean... I mean... If it's possible to analyze all the datasets at the same time, I have to use the raw data and standardize the steps...
Can someone give me a light? (I'm using R)
