>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,combi ne="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 [[alternative HTML version deleted]]