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Topic: Error in `colnames<-`(`*tmp*`, value = c(... (Read 3184 times) previous topic - next topic

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>)
>