Search
Question: gseDO function input
0
gravatar for xr2120
4 months ago by
xr21200
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 4 months ago by Guangchuang Yu810 • written 4 months ago by xr21200
1
gravatar for Guangchuang Yu
4 months ago by
Hong Kong
Guangchuang Yu810 wrote:
ADD COMMENTlink written 4 months ago by Guangchuang Yu810

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 4 months ago by xr21200
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 269 users visited in the last hour