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Messages - Student
2
metaXCMS / Re: Common features
> 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$setBorderWidth(
pwindow$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
Error in function (x) : object 'CommonFeaturesTab.continue' not found
What can I do about this?
4
metaXCMS / Re: Alignment + EICs
I moved the raw data within the XCMS result folder.
5
metaXCMS / Alignment + EICs
Error in xcms:::phenoDataFromPaths(files) : Directory tree must be level
What can I do about this?