'names' attribute [12] must be the same length as the vector [6]
0
0
Entering edit mode
bhgyu ▴ 30
@bhgyu-13069
Last seen 2.7 years ago
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
R xcms vector • 1.4k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi yes correct - 12 data files and 12 distinct names

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 378 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6