Dear R-Users, I am trying to perform network analysis using BioNet. I am having issues with the runFastHeinz function. I extracted the sub network and computed the scores and fed to the function. I even tried to run the function from the example data in the help function. I get the same error. Please help me solve this issue. I tried accessing the igraph.from.graphNEL function from igraph as igraph::igraph.from.graphNEL. But still it didnt fix the error.
library(DLBCL) data(dataLym) data(interactome) interactome <- subNetwork(dataLym$label, interactome) p.values <- dataLym$t.pval names(p.values) <- dataLym$label bum <- fitBumModel(p.values, plot=TRUE) scores <- scoreNodes(network=interactome, fb=bum, fdr=0.0001) module <- runFastHeinz(network=interactome, scores=scores) Error in graph[[9]][[3]] : subscript out of bounds > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_SG LC_NUMERIC=C LC_TIME=en_SG [4] LC_COLLATE=en_SG LC_MONETARY=en_SG LC_MESSAGES=en_SG [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_SG LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hash_2.2.6 DLBCL_1.3.5 BioNet_1.18.0 [4] RBGL_1.34.0 Biobase_2.18.0 BiocGenerics_0.4.0 [7] igraph0_0.5.5-3 maanova_1.28.0 samr_2.0 [10] matrixStats_0.8.12 impute_1.32.0 limma_3.14.4 [13] Rgraphviz_2.2.1 graph_1.36.2 GeneNet_1.2.8 [16] igraph_0.6.6 fdrtool_1.2.11 longitudinal_1.1.8 [19] corpcor_1.6.6 BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.7 DBI_0.2-7 IRanges_1.16.6 [4] parallel_2.15.1 R.methodsS3_1.5.2 RSQLite_0.11.4 [7] stats4_2.15.1 tools_2.15.1 Thanks, Regards, Kishor ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.