>From: Jing Huang [mailto:huangji@ohsu.edu]
>Sent: Wednesday, September 14, 2011 11:00 AM
>To: Tarca, Adi
>Subject: question for you on SPIA package
>Dear Adi,
>I have a new question on SPIA package and have sent it to the mailing list a few days ago. I did not received an answer. I am trying again here by sending you the question directly and hope to get a help. Please forgive me.
>The SPIA package does not support some organism such as C Elegans but I found and downloaded to my computer. I don't know how to  use this file to predict the pathway: here is an example:
>load("/Users/huangji/Downloads/dmeSPIA.RData")
>Here is the R scripts for predicting the pathways:
>res=spia(de=CH,all=CH1,organism="dme",nB=2000,plots=F,beta=NULL,combine="fisher",verbose=F)
>Can you help me?
>Many THANKS
>Jing

Hi Jing,
If you downloaded the pathway data for additional organisms from http://bioinformaticsprb.med.wayne.edu/SPIA/build03212011/ then all you need to do is to copy the file xxxSPIA.RData  file in the extdata folder of the SPIA directory.
(eg. R-2.13.1\library\SPIA\extdata)

Your code should work except perhaps you will get the pathways for Drosophila and not C Elegans. For C Elegans you should use the sce instead of dme. The names of CH and the vector CH1 must be valid ENTREZ IDs for the respective organism.

Adi Tarca

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