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Messages - Student

1
metaXCMS / Re: Common features
The problem is solved by installing earlier versions of R (2.14.2) and metaXCMS (0.1.19).
2
metaXCMS / Re: Common features
Here you can find the detailed information:

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Dutch_Belgium.1252  LC_CTYPE=Dutch_Belgium.1252    LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C                  LC_TIME=Dutch_Belgium.1252   

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

other attached packages:
 [1] RANN_2.2.1          gstat_1.0-16        sp_1.0-8            xcms_1.34.0        mzR_1.4.7          Rcpp_0.10.3        Biobase_2.18.0      BiocGenerics_0.4.0
 [9] RGtk2_2.20.25      cairoDevice_2.19    BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] codetools_0.2-8  grid_2.15.3      intervals_0.14.0 lattice_0.20-13  metaXCMS_0.1.20  spacetime_1.0-4  tools_2.15.3    xts_0.9-3        zoo_1.7-9   

> traceback()
1: function (x)
  {
      mztol <- as.numeric(gtkEntryGetText(CommonFeaturesTab.mz.entry))
      if (is.na(mztol)) {
          dialog <- gtkMessageDialogNew(mainWindow, c("modal",
              "destroy-with-parent"), "error", "ok", "Please enter valid m/z tolerance !n")
          dialog$run()
          dialog$destroy()
          gtkEntrySetText(CommonFeaturesTab.mz.entry, DEFAULT_MZ_DEV)
          return()
      }
      rttol <- as.numeric(gtkEntryGetText(CommonFeaturesTab.rt.entry))
      if (is.na(rttol)) {
          dialog <- gtkMessageDialogNew(mainWindow, c("modal",
              "destroy-with-parent"), "error", "ok", "Please enter valid retention time tolerance !n")
          dialog$run()
          dialog$destroy()
          gtkEntrySetText(CommonFeaturesTab.rt.entry, DEFAULT_RT_DEV)
          return()
      }
      nfiltered <- sapply(xcmsFiles, function(x) nrow(x$filtered))
      if (any(nfiltered == 0)) {
          dialog <- gtkMessageDialogNew(mainWindow, c("modal",
              "destroy-with-parent"), "error", "ok", paste("The filtered dataset #",
              which(nfiltered == 0), " contains no features using the current filtering parameters.n",
              "Please adjust filtering parameters !n", sep = ""))
          dialog$run()
          dialog$destroy()
          return()
      }
      n <- length(xcmsFiles)
      xs <- createXcmsSet()
      pwindow <- gtkWindowNew("toplevel", FALSE)
      pwindow$title <- "Calculating alignment ..."
      pwindow$setBorderWidth(8)
      pwindow$setSizeRequest(400, PROGRESS_BAR_WIDTH)
      pwindow$setPosition("center")
      bp = gtkProgressBarNew()
      pwindow$add(bp)
      bp$setFraction(0.1)
      pwindow$show()
      gtkWait()
      progressCallback <- function(progress) {
          bp$setFraction(progress$group.nearest)
          gtkWait()
      }
      xs@progressCallback <- progressCallback
      xsa <<- group.nearest.meta(xs, mzCheck = mztol, rtCheck = rttol,
          kNN = 20)
      cat("n")
      pwindow$destroy()
      CommonFeaturesTab.continue$setSensitive(TRUE)
      CommonFeaturesTab.save.png$setSensitive(TRUE)
      CommonFeaturesTab.save.pdf$setSensitive(TRUE)
      CommonFeaturesTab.export.commonFeatures.table$setSensitive(TRUE)
      CommonFeaturesTab.export.allFeatures.table$setSensitive(TRUE)
      CommonFeaturesTab.export.commonFeatures.table.detailed$setSensitive(TRUE)
      CommonFeaturesTab.export.allFeatures.table.detailed$setSensitive(TRUE)
      gv <- groupval(xsa, method = "medret", value = "index")
      tmp <- checkSubtract(gv)
      gv <- tmp$gv
      gvbin <<- as.data.frame(!is.na(gv))
      if (ncol(gvbin) > 1 && ncol(gvbin) < 6) {
          dev.set(CommonFeaturesTab.plot.dev)
          plot(1, type = "n", axes = FALSE, xlab = "", ylab = "")
          venn(gvbin)
      }
      else cat("Result has ", ncol(gvbin), " column(s), not showing Venn diagram. n")
      cat("t -->", nrow(gvbin), "common features. n")
  }(<pointer: 0x093e1990>)
3
metaXCMS / Common features
Importing files in metaXCMS and filtering is no problem, but when I try to find the common features (with m/z tolerance 0.01 and retention time tolerance 60s), no Venn diagram is shown and the following message appears in R:
Error in function (x)  : object 'CommonFeaturesTab.continue' not found
What can I do about this?
4
metaXCMS / Re: Alignment + EICs
I am trying to compare 5 XCMS results.
I moved the raw data within the XCMS result folder.
5
metaXCMS / Alignment + EICs
When I want to align my data or produce EICs with metaXCMS, nothing is happening. In R an error message appears:
Error in xcms:::phenoDataFromPaths(files) : Directory tree must be level
What can I do about this?