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Topic: Duplicate 'row.names' ERROR (Read 5112 times) previous topic - next topic

Duplicate 'row.names' ERROR

Hi to all, I notice a strange  error while I run xcmsSet:
Code: [Select]
xset <- xcmsSet(files, method="centWave", nSlaves=4, polarity="positive", prefilter=c(3,100), ppm=5)

In particular, if :
Code: [Select]
files <- list.files(path= myPath, pattern="mzXML", full.names = TRUE, recursive =TRUE)

all works fine but, if:
Code: [Select]
files <- list.files(path= myPath, pattern="mzXML", full.names = FALSE, recursive =TRUE)

the xcmsSet function says:
Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed
In addition: Warning message: non-unique values when setting 'row.names': ‘’ .

If I see the files object, I do not see any duplicate.

    > files
     [1] "Negative/Controllo10.mzXML"    "Negative/Controllo11.mzXML" 
     [3] "Negative/Controllo12.mzXML"    "Negative/Controllo13.mzXML" 
     [5] "Negative/Controllo14.mzXML"    "Negative/Controllo15.mzXML" 
     [7] "Negative/Controllo16.mzXML"    "Negative/Controllo17.mzXML" 
     [9] "Negative/Controllo18.mzXML"    "Negative/Controllo19.mzXML" 
    [11] "Negative/Controllo1.mzXML"    "Negative/Controllo20.mzXML" 
    [13] "Negative/Controllo21.mzXML"    "Negative/Controllo22.mzXML" 
    [15] "Negative/Controllo23.mzXML"    "Negative/Controllo24.mzXML" 
    [17] "Negative/Controllo25.mzXML"    "Negative/Controllo26.mzXML" 
    [19] "Negative/Controllo27.mzXML"    "Negative/Controllo28.mzXML" 
    [21] "Negative/Controllo29.mzXML"    "Negative/Controllo2.mzXML"   
    [23] "Negative/Controllo30.mzXML"    "Negative/Controllo31.mzXML" 
    [25] "Negative/Controllo32.mzXML"    "Negative/Controllo33.mzXML" 
    [27] "Negative/Controllo34.mzXML"    "Negative/Controllo35.mzXML" 
    [29] "Negative/Controllo36.mzXML"    "Negative/Controllo37.mzXML" 
    [31] "Negative/Controllo38.mzXML"    "Negative/Controllo39.mzXML" 
    [33] "Negative/Controllo3.mzXML"    "Negative/Controllo40.mzXML" 
    [35] "Negative/Controllo41.mzXML"    "Negative/Controllo42.mzXML" 
    [37] "Negative/Controllo43.mzXML"    "Negative/Controllo44.mzXML" 
    [39] "Negative/Controllo45.mzXML"    "Negative/Controllo46.mzXML" 
    [41] "Negative/Controllo47.mzXML"    "Negative/Controllo48.mzXML" 
    [43] "Negative/Controllo49.mzXML"    "Negative/Controllo4.mzXML"   
    [45] "Negative/Controllo50.mzXML"    "Negative/Controllo51.mzXML" 
    [47] "Negative/Controllo52.mzXML"    "Negative/Controllo53.mzXML" 
    [49] "Negative/Controllo54.mzXML"    "Negative/Controllo55.mzXML" 
    [51] "Negative/Controllo56.mzXML"    "Negative/Controllo57.mzXML" 
    [53] "Negative/Controllo58.mzXML"    "Negative/Controllo59.mzXML" 
    [55] "Negative/Controllo5.mzXML"    "Negative/Controllo60.mzXML" 
    [57] "Negative/Controllo6.mzXML"    "Negative/Controllo7.mzXML"   
    [59] "Negative/Controllo8.mzXML"    "Negative/Controllo9.mzXML"   
    [61] "Positive/Positivo1_rip1.mzXML" "Positive/Positivo1_rip2.mzXML"
    [63] "Positive/Positivo1_rip3.mzXML" "Positive/Positivo2_rip1.mzXML"
    [65] "Positive/Positivo2_rip2.mzXML" "Positive/Positivo2_rip3.mzXML"
    [67] "Positive/Positivo3_rip1.mzXML" "Positive/Positivo3_rip2.mzXML"
    [69] "Positive/Positivo3_rip3.mzXML" "Positive/Positivo4_rip1.mzXML"
    [71] "Positive/Positivo4_rip2.mzXML" "Positive/Positivo4_rip3.mzXML"
    [73] "Positive/Positivo5_rip1.mzXML" "Positive/Positivo5_rip2.mzXML"
    [75] "Positive/Positivo5_rip3.mzXML"
    >

Any suggestion??

EDIT
> traceback()
6: stop("duplicate 'row.names' are not allowed")
5: `row.names<-.data.frame`(`*tmp*`, value = value)
4: `row.names<-`(`*tmp*`, value = value)
3: `rownames<-`(`*tmp*`, value = c(NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
  NA_character_, NA_character_, NA_character_))
2: phenoDataFromPaths(files)
1: xcmsSet(files, method = "centWave", nSlaves = 4, polarity = "positive",
      ppm = 5)


P.S. Merry XMas :D

Re: Duplicate 'row.names' ERROR

Reply #1 –
I've never seen this problem before.
It looks like something went wrong during alignment, the rownames should correspond to mzRT
and not be NA.
did you resolve the other problem you had ?  maybe there is really something weird going on with you R/xcms installation.