Run Gene Pattern (GenePattern) from R

[bmuchmore]

Simple question, but one I have struggled with due to weak R skills.

I have set up a local instance of GenePattern with no issues i.e. the GUI works fine. In addition, I can follow this tutorial that links R and Gene Pattern with no problems:

http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/programmers/sections/gp_r

My problem arises when I go off and try to run other modules with my own code. Would someone be willing to share some example R code that can call a GenePattern module? I just can't find any other examples (specific or generic) on the web that will help me teach myself.

Thanks.

-Brian Muchmore

[bhill]

This question has been answered on Biostars
https://www.biostars.org/p/134218/