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Hi all,
I'm a little bit confused about the input of gseDO. In DOSE vignette, the input of gseGO is a gene list called "geneList". In this gene list, for each gene, there is a corresponding log fold change. But how can we calculate the correlation between each gene and phenotype if the input is just one single number for each gene? I'd appreciate if anyone could help. Thanks.
Hi Guangchuang,
Thanks for your prompt response. I have figured out this issue. I checked your GitHub page, and noted that gseDO permutates the gene list to get empirical distribution of ES. I thought it permutates phenotypes. That's why I get confused.
Thanks for your help.
HI Hi Guangchuang.
Is it possible to set the organism to mouse with OrgDb = "org.Mm.eg.db"? or is it just for human?
Best regards
Raian
no, see https://support.bioconductor.org/p/125555/#125570.