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Question: GO slim data for GAGE GSEA analysis
0
gravatar for rubi
15 months ago by
rubi70
rubi70 wrote:

Hi,

 

Is it possible to use GO slim data in a GSEA with GAGE?

 

ADD COMMENTlink modified 12 months ago by Guangchuang Yu800 • written 15 months ago by rubi70
1
gravatar for Luo Weijun
15 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
I understand GO slim is just a concise version of GO with fine grained terms removed. GAGE definitely works with GO slim data in the right format, i.e. a named list where each element is a vector of member genes mapping to a GO term (or a pathway). Note that you don’t have to make GO slim data by youself. You can create the complete GO data with go.gsets function from the package, then use set.size=c(10, Inf) when calling gage. This way, you are creating a GO slim on the fly by removing small GO terms with less than 10 genes mapped. Of course, you may also set the upper limit like set.size=c(10, 1000) as to remove GO terms which are too general. For more details please check the gage documentation: http://bioconductor.org/packages/release/bioc/html/gage.html
ADD COMMENTlink written 15 months ago by Luo Weijun1.4k
0
gravatar for rubi
12 months ago by
rubi70
rubi70 wrote:

Hi Lou,

I think there's another difference between applying a limited set.size, as you suggest, and GO slim. GO slim is also slim on redundancy between categories. Is there a way to test for non-redundant categories using GAGE?

ADD COMMENTlink written 12 months ago by rubi70
0
gravatar for Luo Weijun
12 months ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:

gage package does provide a function, esset.grp(), to extract a non-redundant signcant gene set list and

related data from gage() results. For details:

library(gage)

?esset.grp

ADD COMMENTlink written 12 months ago by Luo Weijun1.4k
0
gravatar for Guangchuang Yu
12 months ago by
Hong Kong
Guangchuang Yu800 wrote:

another alternative solution is using GO semantic similarity to remove redundant terms, see https://guangchuangyu.github.io/2015/10/use-simplify-to-remove-redundancy-of-enriched-go-terms/

ADD COMMENTlink written 12 months ago by Guangchuang Yu800
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