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:
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.
If you've already read the R Programming Guide section, one other thing you can do is to generate the R code to call the module you've created. You will then be able to paste it into your R program to run the module.
To do this, log in to your GenePattern server and select the module you would like to call through R. On the right-hand side of the module's title you will see a gear icon. Click this icon and select "R code". You will then see a line of R code that you can use to call that module, when you substitute your desired parameters. (This assumes you have also included the GenePattern R library and set up your R script as described in the programmer's guide.)
If this doesn't work, can you paste an example of the call you are making that isn't working?
Thanks for the input Michael. I tried what you suggested and it worked without a hitch. I did the same thing yesterday, but for whatever reason it was not working. What I give real credit to, however, is RKWard, which allowed me to investigate the various functions in the GenePattern library, so I could understand what all the calls were doing. Previously, I had not found any documentation for that. Thanks again for your input.
Thanks for the input Michael. I tried what you suggested and it worked without a hitch. I did the same thing yesterday, but for whatever reason it was not working. What I give real credit to, however, is RKWard, which allowed me to investigate the various functions in the GenePattern library, so I could understand what all the calls were doing. Previously, I had not found any documentation for that. Thanks again for your input.
-Brian
Thanks Brian - glad it's working, and thanks for the tip about RKWard!
Best,
Michael