Question: gseDO function input
gravatar for xr2120
7 months ago by
xr21200 wrote:

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.

ADD COMMENTlink modified 7 months ago by Guangchuang Yu960 • written 7 months ago by xr21200
gravatar for Guangchuang Yu
7 months ago by
Hong Kong
Guangchuang Yu960 wrote:
ADD COMMENTlink written 7 months ago by Guangchuang Yu960

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 REPLYlink written 7 months ago by xr21200
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