I wanted to use DART (Denoising Algorithm based on Relevance network Topology). I have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200 genes, names are EntrezGeneIDs. So I wanted to get the activity scores, but they are always "NA" using pred.o<-PredActScore(prNet.o$pradjMC,prNet.o$signMC,data) and there are warnings(): 50: mean(<data.frame>) is deprecated. Use colMeans() or sapply(*, mean) instead. So my question is: where did I a mistake, maybe my data has not the right format, but I get normal results by using: print(evalNet.o$netcons) And the next problem is, that the program only runs, if the first column of my expression data is that one with the EntrezGeneID, deleting that column resulting in the failure: Failure in if (netconsist > netconsist.v[4]) { : Missing value, where TRUE / FALSE needed -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

Dear Martin, Thanks for your questions, but I can't reproduce this from the descriptions. Could you provide a small reproducible example (for cut-and-paste) and the complete sessionInfo() output? It may be that the input data are not in the expected format or types; see the vignette or ?DoDART, and have a look at the example dataset: > data(dataDART) > head(dataDART$data) > head(dataDART$sign) best wishes, Katherine ________________________________________ From: Martin Garbe [guest] [guest@bioconductor.org] Sent: 28 February 2014 18:05 To: bioconductor at r-project.org; manrap91 at web.de Cc: Lawler, Katherine Subject: DART I wanted to use DART (Denoising Algorithm based on Relevance network Topology). I have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200 genes, names are EntrezGeneIDs. So I wanted to get the activity scores, but they are always "NA" using pred.o<-PredActScore(prNet.o$pradjMC,prNet.o$signMC,data) and there are warnings(): 50: mean(<data.frame>) is deprecated. Use colMeans() or sapply(*, mean) instead. So my question is: where did I a mistake, maybe my data has not the right format, but I get normal results by using: print(evalNet.o$netcons) And the next problem is, that the program only runs, if the first column of my expression data is that one with the EntrezGeneID, deleting that column resulting in the failure: Failure in if (netconsist > netconsist.v[4]) { : Missing value, where TRUE / FALSE needed -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.