Question

gseDO function input

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xr2120 • 0

@xr2120-13720

Last seen 6.6 years ago

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.

DOSE clusterprofiler • 3.7k views

ADD COMMENT • link updated 7.3 years ago by Guangchuang Yu ★ 1.2k • written 7.3 years ago by xr2120 • 0

score 1 · Answer 1 · 2017-08-11

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Guangchuang Yu ★ 1.2k

@guangchuang-yu-5419

Last seen 24 days ago

China/Guangzhou/Southern Medical Univer…

see https://github.com/GuangchuangYu/DOSE/wiki/how-to-prepare-your-own-geneList.

ADD COMMENT • link 7.3 years ago Guangchuang Yu ★ 1.2k

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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.

ADD REPLY • link 7.3 years ago xr2120 • 0

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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

ADD REPLY • link 5.1 years ago raianbio • 0

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no, see https://support.bioconductor.org/p/125555/#125570.

ADD REPLY • link 5.1 years ago Guangchuang Yu ★ 1.2k