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Looking over your code I see that you are using the Fisher exact test (FET). Several assumptions of the FET are not meet when testing gene sets by GO annotation (cite). If this is for a school project FET is good enough. However, if this data set is for publication I would recommend using a different analysis. I don't know what your data looks like and the ...


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If you are adding phenol-chloroform extracted tRNA then that is a carrier for the precipitation steps. Some people use linear acrylamide for the same purpose.



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