Skip to main content

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - hugocarlos

1
metaXCMS / Error in `colnames<-`(`*tmp*`, value = c(...
Hi there,

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>)
>