1
metaXCMS / Error in `colnames<-`(`*tmp*`, value = c(...
I'm using the library metaXCMS in R in Windows.
Using the published data set from: http://metlin.scripps.edu/data/metaXCMS ... stdata.zip I am using the option to subtract one of the pairwise comparisons (VNG2094G_vs_URA3), I am considering the URA3 as controls.
When I try to download the csv for All features (detailed) I receive the following error:
Error in `colnames<-`(`*tmp*`, value = c("VNG1179c_H2O_1", "VNG1179c_H2O_2", :
length of 'dimnames' [2] not equal to array extent
All parameter were as default.
I have the same Error using my own data and I need the Intensity values for each of my replicates once they are aligned.
Do you have a solution for that?
Thanks,
PS The following is the sessionInfo and the traceback:
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] metaXCMS_0.1.20 RANN_2.3.0 gstat_1.0-18 xcms_1.38.0 mzR_1.8.1
[6] Rcpp_0.11.0 Biobase_2.22.0 BiocGenerics_0.8.0 RGtk2_2.20.25 cairoDevice_2.19
loaded via a namespace (and not attached):
[1] codetools_0.2-8 intervals_0.14.0 lattice_0.20-23 sp_1.0-14 spacetime_1.0-9
[6] tools_3.0.2 xts_0.9-7 zoo_1.7-10
> traceback()
3: `colnames<-`(`*tmp*`, value = c("VNG1179c_H2O_1", "VNG1179c_H2O_2",
"URA3_control_H2O_1", "URA3_control_H2O_2", "VNG1816G_H2O_1",
"VNG1816G_H2O_2", "URA3_control_H2O_1", "URA3_control_H2O_2",
"VNG2094G_H2O_1", "VNG2094G_H2O_2", "URA3_control_H2O_1", "URA3_control_H2O_2"
))
2: getAllPeaks(commonOnly = FALSE)
1: (function (x)
{
dialog <- gtkFileChooserDialog("Save all features table (detailed)",
NULL, "save", "gtk-cancel", GtkResponseType["cancel"],
"gtk-open", GtkResponseType["accept"])
dialog$showAll()
if (dialog$run() == GtkResponseType["accept"]) {
filename <- dialog$getFilename()
if (file.extension(filename) != "csv")
filename <- paste(filename, "csv", sep = ".")
p <- getAllPeaks(commonOnly = FALSE)
write.csv(p, file = filename, row.names = FALSE)
}
dialog$destroy()
})(<pointer: 0x11c4bc60>)
>