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,plot s=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 -- Sent via the guest posting facility at bioconductor.org.

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@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,plot s=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 -- Sent via the guest posting facility at bioconductor.org.