Hi Yemi,
I have posted recently an updated version of SPIA (2.10.0)  (available in the devel branch) that you can use to run SPIA on any organism available in KEGG starting with KEGG KGML files. It seems that there is a KEGGREST package from the bioc team that can help you get those files. Below are a few lines that I borrowed from Dan Tenenbaum showing how to get the files:


library(KEGGREST)

keggList("pathway")

#or filter by organism (or T number):

keggList("pathway", "hsa")

keggGet("hsa05130", "kgml")


Using the files is described in the new SPIA vignette.
Now in terms of adjustments for use with RNA-seq, we are currently working on some solutions but we have no method ready yet. You could for instance use the goseq package to get the over-representation p-values for each pathway  (adjusted for some types of biases) and use those to replace the PNDE from SPIA output. You can further combine the biases adjusted pNDE with pPERT as explained in the vignette.

Thanks,
Adi


Adi Laurentiu TARCA, Ph.D.
Assistant Professor (Research),
Department of Computer Science & Center for Molecular Medicine and Genetics, Wayne State University,
Director, Bioinformatics and Computational Biology Unit,  Perinatology Research Branch (NICHD),
3990 John R., Office 4809,
Detroit, Michigan 48201
Tel: 1-313-5775305

From: oyeyemi ajayi [mailto:yemijay2002@yahoo.com]
Sent: Thursday, February 28, 2013 10:22 AM
To: Tarca, Adi
Subject: SPIA algorithm organisms not included already in the SPIA package

Hi,
I'm really happy about the novelty of the spia package, available for use in bioconductor. I have some rna-seq data on cattle and I want to adopt your package for pathway analysis. In the package, the SPIA algorithm uses KEGG signaling pathway data for hsa and mmu organisms were only available for use but not for other organisms. I followed the link but can't access it.

Can spia be used for rna-seq reads? If yes,what are the modifications we need to do to have it running using SPIA?

Yemi.

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