Question: gseDO function input
gravatar for xr2120
9 weeks 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 9 weeks ago by Guangchuang Yu700 • written 9 weeks ago by xr21200
gravatar for Guangchuang Yu
9 weeks ago by
Hong Kong
Guangchuang Yu700 wrote:
ADD COMMENTlink written 9 weeks ago by Guangchuang Yu700

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 9 weeks ago by xr21200
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