While using gene_set_enrichment @sparthib noticed she had a significant result for a layer enrichment/gene-set pair with an OR = 0. The gene list she was using had no overlapping genes with genes enriched for in WM, so the OR=0, but the pval < 0.05. Currently the fisher.test is using the default alternative = "two.sided" so any OR != 1 can be significant so this result is technically correct but I think deviates from described use of this function, where we are looking for where gene sets are enriched or over represented in the models significant genes, where the OR > 1. I propose we change to using fisher.test(alternative = "greater") to avoid detecting OR < 1.
I also included a warning message for genes sets with n < 25 as in practice we thought they had too little power for good results.
While using
gene_set_enrichment@sparthib noticed she had a significant result for a layer enrichment/gene-set pair with an OR = 0. The gene list she was using had no overlapping genes with genes enriched for in WM, so the OR=0, but the pval < 0.05. Currently thefisher.testis using the defaultalternative = "two.sided"so any OR != 1 can be significant so this result is technically correct but I think deviates from described use of this function, where we are looking for where gene sets are enriched or over represented in the models significant genes, where the OR > 1. I propose we change to usingfisher.test(alternative = "greater")to avoid detecting OR < 1.I also included a warning message for genes sets with n < 25 as in practice we thought they had too little power for good results.