global test with .gmt file

Question

[lkarki2000]

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

[Devon Ryan]

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?

[lkarki2000]

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

Laxman

Answer 1

[GANI]

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.