geo2r to replicate publication results

Question

[jiwpark00]

Hi, so I just started using GEO2R as a quick way to run through some comparisons in the datasets available on NCBI's GEO database, and I have few questions. First, when I run GEO2R at the default setting, I'm getting a list of differential expressed genes but the top list of genes that the original paper (where the dataset is from) identified do not all show up. This is concerning because I wonder if GEO2R is not very accurate - is that true? I know it doesn't do all the normalization and other statistical adjustments, but my take was, the list should be similar (I don't expect values like logFC to be same but just the list).

Thank you.

Answer 1

[TriS]

the analysis run by GEO2R is a basic analysis made to fit multiple dataset, in order to replicate the results from the paper you should read the methods in the paper and try to replicate that analysis. is not that GOE2R is not "accurate", it's probably just a different analysis