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1
December 01, 2014, 05:04:00 PM
Hi Steffen, Sorry it took me two days to get github devtools in R running on Windows. Finally it works in R on cmd shell but not in the windows R console.... Do not ask me why... Yes it works: > rsP@rules name nmol charge massdiff oidscore quasi ips 1 [M+H]+ 1 1 1.007276 1 1 1.00 5 [M+Na]+ 1 1 22.989218 5 1 1.00 6 [M+2Na-H]+ 1 1 44.971160 6 0 0.25 7 [M+H-H20]+ 1 1 -17.008024 7 0 0.25 Well I guess 6 is very very unlikely. Is there a parameter that can omit ion 6? Or should I directly delete it with rsP@rules[c(1,2,4),]->rsP@rules Thanks for your help, Andre
2
November 14, 2014, 03:00:52 PM
I try the following: > rsP <- new("ruleSet") > rsP@ionlistfile <- "ions_pos.csv" > rsP@neutraladditionfile <- "neutraladdition.csv" > rsP@neutrallossfile <- "neutralloss.csv" > rsP <- readLists(rsP) > rsP <- setDefaultParams(rsP) > rsP <- generateRules(rsP) Fehler in if (neutraladdition[i, 1] == "NaCOOH") { : Fehlender Wert, wo TRUE/FALSE nötig ist which is because neutraladdition.csv just has the header and no entries which creates an empty slot of neutraladdition. I do not want to allow a neutral addition in my rule set. Is there a possibility to fix that? I guess the problem is in the section "## Erzeuge Neutral" of ruleSet.R Many Thanks, Andre ------ > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 [4] LC_NUMERIC=C LC_TIME=German_Germany.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ProbMetab_1.0 rjson_0.2.14 multtest_2.20.0 XML_3.98-1.1 [5] RCurl_1.95-4.3 bitops_1.0-6 hwriter_1.3.2 RCytoscape_1.14.0 [9] XMLRPC_0.3-0 graph_1.42.0 GeneNet_1.2.10 fdrtool_1.2.12 [13] longitudinal_1.1.9 corpcor_1.6.6 RcppArmadillo_0.4.400.0 CAMERA_1.20.0 [17] igraph_0.7.1 xcms_1.40.0 Biobase_2.24.0 BiocGenerics_0.10.0 [21] mzR_1.10.7 Rcpp_0.11.2 loaded via a namespace (and not attached): [1] acepack_1.3-3.3 cluster_1.15.3 codetools_0.2-9 foreign_0.8-61 Formula_1.1-2 [6] grid_3.1.0 Hmisc_3.14-5 lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-34 [11] nnet_7.3-8 RBGL_1.40.1 RColorBrewer_1.0-5 rpart_4.1-8 splines_3.1.0 [16] stats4_3.1.0 survival_2.37-7 tools_3.1.0 >
3
June 17, 2014, 02:50:50 PM
plotEICs(anP.group.iso.corr.add, pspec=2, maxlabel=5) results in https://www.dropbox.com/s/4ovljepz1c99q7u/maxlabel5.eps and plotEICs(anP.group.iso.corr.add, pspec=2, maxlabel=10) results in https://www.dropbox.com/s/56aiv7ltkczfv ... abel10.eps As you can see the color labels are pointing to different peaks in the two versions of the same spectra. ---- > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ProbMetab_1.0 rjson_0.2.13 multtest_2.20.0 XML_3.98-1.1 RCurl_1.95-4.1 bitops_1.0-6 [7] hwriter_1.3 RCytoscape_1.14.0 XMLRPC_0.3-0 graph_1.42.0 GeneNet_1.2.9 fdrtool_1.2.12 [13] longitudinal_1.1.9 corpcor_1.6.6 RcppArmadillo_0.4.300.0 CAMERA_1.20.0 igraph_0.7.0 xcms_1.40.0 [19] Biobase_2.24.0 BiocGenerics_0.10.0 mzR_1.10.0 Rcpp_0.11.1 loaded via a namespace (and not attached): [1] cluster_1.15.2 codetools_0.2-8 Formula_1.1-1 grid_3.1.0 Hmisc_3.14-4 lattice_0.20-29 latticeExtra_0.6-26 [8] MASS_7.3-33 RBGL_1.40.0 RColorBrewer_1.0-5 splines_3.1.0 stats4_3.1.0 survival_2.37-7 tools_3.1.0