[BioC] SPIA

[Tarca, Adi]

Hi Martin,
Not all pathways end up being parsed and analyzed. There is a minimum number of connections that are needed to make any use of the topology. For instance if you look in the hsa03030.xml file you will see no relation (edge) between any node, as opposed to another random pathway (hsa05330) that has some relations defined. So if you are interested in those pathways, use general gene set analysis methods (see PLoS ONE 8(11): e79217 for a comparisons of methods available in Bioconductor).
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

-----Original Message-----
From: Martin [guest] [mailto:guest at bioconductor.org] 
Sent: Thursday, March 06, 2014 7:34 AM
To: bioconductor at r-project.org; mgarbe1 at hs-mittweida.de
Cc: Tarca, Adi
Subject: SPIA


So my question is, why can't I integrate hsa03030.xml,hsa03410.xml,hsa03420.xml,hsa03430.xml,hsa03440.xml
hsa03450.xml,hsa04520.xml
in the SPIA hsaSPIA.RData file?

makeSPIAdata(kgml.path=mydir,organism="hsa",out.path="./")
[1] TRUE

But if I run
spia(de=diff_exp,all=all_exp,organism="hsa",data.dir="./",nB=2000,plots=FALSE,beta=NULL,combine="fisher",verbose=FALSE)

the pathways don't exist in the table.

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SPIA_2.15.2      KEGGgraph_1.14.0 graph_1.36.2     XML_3.95-0.1    

loaded via a namespace (and not attached):
[1] BiocGenerics_0.4.0 stats4_2.15.2      tools_2.15.2   

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