gseDO function input
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xr2120 • 0
@xr2120-13720
Last seen 3.5 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 • 1.3k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…
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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. 

 

 

 

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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

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