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Meta-analyses to combine significant genes #1
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Hey @inestm28. Thanks for your questions. I don't remember much about this analysis, so the source code is probably the best reference for the methods. Here are some additional places to look.
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The Sorry if these answers don't address everything. Feel free to continue using this issue to leave your notes and conclusions for these questions. |
I was looking into your code at https://github.com/dhimmel/stargeo/blob/master/combine.ipynb.
Could you tell me where the file 'balanced_permutation.tsv.gz' comes from /is downloaded from?
And just to make sure, this code uses only the p-values in the "multipletests" method, right?
So, it first gets all the significant genes from each independent study, then creates corrected p-values and after selects the genes that have "up" direction through the fold-change? I'm not sure how the process goes. I would really appreciate if you could help me, please.
And I read in this paper https://doi.org/10.1093/bib/bbaa019, that random effects models are used when the gene is significant in all studies. So it is not used for when it's not in some of the studies, right?
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