Question: gseDO function input
0
gravatar for xr2120
2.3 years 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.

clusterprofiler dose • 863 views
ADD COMMENTlink modified 2.3 years ago by Guangchuang Yu1.1k • written 2.3 years ago by xr21200
Answer: gseDO function input
1
gravatar for Guangchuang Yu
2.3 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
ADD COMMENTlink written 2.3 years ago by Guangchuang Yu1.1k

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 2.3 years ago by xr21200

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 REPLYlink written 5 weeks ago by raianbio0

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

ADD REPLYlink written 5 weeks ago by Guangchuang Yu1.1k
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