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Question: 'names' attribute [12] must be the same length as the vector [6]
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gravatar for bhgyu
3 months ago by
bhgyu30
bhgyu30 wrote:
x <- findChromPeaks(raw, param = cwp)
Error in names(res) <- nms : 
  'names' attribute [12] must be the same length as the vector [6]

I don't understand the error above. I can't seem to figure out what this refers to or how to fix it? Happens on xcms. Strange though, this same code worked fine on a different data set. Any ideas to check or fix it? Many thanks!

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RColorBrewer_1.1-2   xcms_2.99.10         MSnbase_2.3.14       ProtGenerics_1.9.1   mzR_2.11.11         
[6] Rcpp_0.12.13         BiocParallel_1.11.13 Biobase_2.37.2       BiocGenerics_0.23.4 

loaded via a namespace (and not attached):
 [1] compiler_3.4.0         BiocInstaller_1.27.6   plyr_1.8.4             iterators_1.0.8        tools_3.4.0           
 [6] zlibbioc_1.23.0        MALDIquant_1.16.4      digest_0.6.12          preprocessCore_1.39.3  tibble_1.3.4          
[11] gtable_0.2.0           lattice_0.20-35        rlang_0.1.2            Matrix_1.2-9           foreach_1.4.3         
[16] S4Vectors_0.15.14      IRanges_2.11.19        stats4_3.4.0           multtest_2.33.0        grid_3.4.0            
[21] impute_1.51.0          snow_0.4-2             survival_2.41-3        XML_3.98-1.9           RANN_2.5.1            
[26] limma_3.33.14          ggplot2_2.2.1          MASS_7.3-47            splines_3.4.0          scales_0.5.0          
[31] pcaMethods_1.69.0      codetools_0.2-15       MassSpecWavelet_1.43.0 mzID_1.15.0            colorspace_1.3-2      
[36] affy_1.55.0            lazyeval_0.2.0         munsell_0.4.3          doParallel_1.0.11      vsn_3.45.2            
[41] affyio_1.47.1  

From another thread, I think it may be an issue with the "processing" data in processingData, but how do I change it to a character since it's part of a S4 class object? Thanks!

..@ processingData        :Formal class 'MSnProcess' [package "MSnbase"] with 10 slots
  .. .. ..@ files            : chr [1:12] "SJ55.CDF" "SJ56.CDF" "SJ57.CDF" "SJ58.CDF" ...
  .. .. ..@ processing       : chr "Data loaded [Wed Oct 25 17:59:52 2017]"
  .. .. ..@ merged           : logi(0) 
  .. .. ..@ cleaned          : logi(0) 
  .. .. ..@ removedPeaks     : chr(0) 
  .. .. ..@ smoothed         : logi NA
  .. .. ..@ trimmed          : num(0) 
  .. .. ..@ normalised       : logi(0) 
  .. .. ..@ MSnbaseVersion   : chr "2.3.14"
  .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slot
  .. .. .. .. ..@ .Data:List of 1
  .. .. .. .. .. ..$ : int [1:3] 0 1 3
ADD COMMENTlink modified 3 months ago • written 3 months ago by bhgyu30

What type of object is raw? I'm puzzled by this error, because names(res) <- nms is never called in xcms, but it is called in the commonFeatureNames function for MSnSet objects in MSnbase - raw should however be an OnDiskMSnExp object.

ADD REPLYlink written 3 months ago by Johannes Rainer1.2k

It's this. It's an odd error especially cause I've run this with a similar dataset without these issues before...
class(raw)
[1] "OnDiskMSnExp"
attr(,"package")
[1] "MSnbase"

 

 

ADD REPLYlink written 3 months ago by bhgyu30

And you've got a data set consisting of 12 files, right? Are these all distinct files, i.e. have different file names?
 

ADD REPLYlink written 3 months ago by Johannes Rainer1.2k

Hi yes correct - 12 data files and 12 distinct names

ADD REPLYlink written 3 months ago by bhgyu30
1

Without getting hands on the data it is pretty hard to say what's going on and where the problem is.

ADD REPLYlink written 3 months ago by Johannes Rainer1.2k
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