Question: global test with .gmt file
0
gravatar for lkarki2000
5.9 years ago by
lkarki20000
United States
lkarki20000 wrote:

I am having problem with global test analysis in r with my data. I have my gene sets in .gmt file format. I could not apply global test as described in global test package information.

Laxman

R • 1.2k views
ADD COMMENTlink modified 5.9 years ago by GANI220 • written 5.9 years ago by lkarki20000

When you say, "could not apply", what exactly do you mean? Do you get an error? If so, what was the command and what was the error message?

ADD REPLYlink written 5.9 years ago by Devon Ryan94k

I have no clue how to do global test with my gmt file.

Laxman

ADD REPLYlink written 5.9 years ago by lkarki20000
1
gravatar for GANI
5.9 years ago by
GANI220
United States
GANI220 wrote:

The GMT (.gmt) format does not work in the global test package. You need provide either a Matrix or ExpressionSet object for the gt function to work. Essentially if you skip the first two lines while reading the GMT file into R, you should be able convert it into a matrix without any issue.

ADD COMMENTlink modified 3 months ago by RamRS26k • written 5.9 years ago by GANI220
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