Converting Synapter object output into a MSnbase-compatible object
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@dianaschreier-8621
Last seen 5.7 years ago
United States

Hello everyone, 

I am new to R and have a question regarding converting the synapter object output that I created into a MSnbase compatible object.

I loaded my synapter object output into R and is labeled obj. To do the conversion I followed the guidelines provided in this pdf (http://www.bioconductor.org/packages/release/bioc/vignettes/synapter/inst/doc/synapter.pdf) under heading 3.1 Applying the Top 3 approach. 

 I typed: 

> X <- as(obj, "MSnSet")

but I got an error message like this:

Error in value[[3L]](cond) : undefined columns selected
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?

I am not exactly sure what this means, or what I should do next. 

Thank you

synapter msnbase • 1.5k views
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@laurent-gatto-5645
Last seen 2 days ago
Belgium

Indeed, precursor.Mobility is missing - I assume that your experiment you do not have ion mobility, which explains the absence of that column.

I have pushed a new development version (1.11.1) that should make it work for you; it should become available within 24 hours. Let me know if this update does not fix your issue; if it does, please mark this question as answered.

Best wishes,

Laurent

 

 

 

 

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@dianaschreier-8621
Last seen 5.7 years ago
United States

Hello, 

I did the data analysis using synapter 1.11.1 and again used the .rda output as obj and I got a different error message: 

> x <- as(obj, "MSnSet")

Error in `[.data.frame`(from$MatchedEMRTs, , cols) : 

  undefined columns selected

I am not exactly sure what this means. Do you have any thoughts?

 

Thank you, 

Diana

 

 

 

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Synapter 1.11.1 doesn't completely fix the problem. Please try the new 1.11.2 that you could find on: https://github.com/lgatto/synapter/releases/tag/1.11.2

EDIT: please install it via biocLite("lgatto/synapter@1.11.2")

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It worked! Thank you for all of your help Laurent and Sebastian, I really appreciate it. 

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Thanks, Sebastian. Latest version also committed to the Bioconductor svn server, and should be available within 24 hours.

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@laurent-gatto-5645
Last seen 2 days ago
Belgium
>Hello everyone, I am new to R and have a question regarding converting >the synapter object output that I created into a MSnbase compatible >object. I loaded my synapter object output into R and is labeled obj. >To do the conversion I followed the guidelines provided in this pdf >(http://www.bioconductor.org/packages/release/bioc/vignettes/synapter/inst/doc/synapter.pdf) >under heading 3.1 Applying the Top 3 approach. I typed: > X <- >as(obj, "MSnSet") but I got an error message like this: Error in >value[[3L]](cond) : undefined columns selected AnnotatedDataFrame >'initialize' could not update varMetadata: perhaps pData and >varMetadata are inconsistent? I am not exactly sure what this means, or >what I should do next. The conversion from a Synapter data object (obj above) to an MSnSet data object (X above) fails, but it's not clear why. Could you briefly describe how you created obj. In addition, could you provide the output of sessionInfo(). Laurent PS: I'm currently travelling and might not he able to get back to you promptly.
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@laurent-gatto-5645
Last seen 2 days ago
Belgium
>Hello everyone, I am new to R and have a question regarding converting >the synapter object output that I created into a MSnbase compatible >object. I loaded my synapter object output into R and is labeled obj. >To do the conversion I followed the guidelines provided in this pdf >(http://www.bioconductor.org/packages/release/bioc/vignettes/synapter/inst/doc/synapter.pdf) >under heading 3.1 Applying the Top 3 approach. I typed: > X <- >as(obj, "MSnSet") but I got an error message like this: Error in >value[[3L]](cond) : undefined columns selected AnnotatedDataFrame >'initialize' could not update varMetadata: perhaps pData and >varMetadata are inconsistent? I am not exactly sure what this means, or >what I should do next. The conversion from a Synapter data object (obj above) to an MSnSet data object (X above) fails, but it's not clear why. Could you briefly describe how you created obj. In addition, could you provide the output of sessionInfo(). Laurent PS: I'm currently travelling and might not he able to get back to you promptly.
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@dianaschreier-8621
Last seen 5.7 years ago
United States

Laurent, 

I created obj through the synergise function. In the output file that I specified there was an rda file titled SynapterObject. I opened this and was asked "Do you want to load the R data file “C:/Users/Diana/Documents/Synapter/Aug17/SynapterObject.rda” into the global environment?" I clicked yes and it was made available as "obj" in RStudio.

 

This is my sessionInfo() output: 

R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] tcltk2_1.2-11       synapter_1.10.0     MSnbase_1.16.2     
[4] ProtGenerics_1.0.0  BiocParallel_1.2.20 mzR_2.2.1          
[7] Rcpp_0.12.0         Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2    XVector_0.8.0        
 [3] BiocInstaller_1.18.4  futile.logger_1.4.1  
 [5] plyr_1.8.3            iterators_1.0.7      
 [7] futile.options_1.0.0  tools_3.2.1          
 [9] zlibbioc_1.14.0       MALDIquant_1.12      
[11] digest_0.6.8          preprocessCore_1.30.0
[13] gtable_0.1.2          lattice_0.20-33      
[15] foreach_1.4.2         proto_0.3-10         
[17] hwriter_1.3.2         knitr_1.10.5         
[19] stringr_1.0.0         Biostrings_2.36.3    
[21] S4Vectors_0.6.3       IRanges_2.2.7        
[23] multtest_2.24.0       stats4_3.2.1         
[25] grid_3.2.1            qvalue_2.0.0         
[27] impute_1.42.0         survival_2.38-3      
[29] XML_3.98-1.3          limma_3.24.15        
[31] cleaver_1.6.0         ggplot2_1.0.1        
[33] reshape2_1.4.1        lambda.r_1.1.7       
[35] magrittr_1.5          splines_3.2.1        
[37] scales_0.2.5          pcaMethods_1.58.0    
[39] codetools_0.2-14      MASS_7.3-43          
[41] mzID_1.6.0            colorspace_1.2-6     
[43] stringi_0.5-5         affy_1.46.1          
[45] munsell_0.4.2         doParallel_1.0.8     
[47] vsn_3.36.0            affyio_1.36.0    

 

Thank you, 

Diana

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Thanks, that all looks fine. Could you give me the output of the following line colnames(obj$MatchedEMRTs). I think some of the expected column names, that are used during the conversion to an MSnSet are missing.

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@dianaschreier-8621
Last seen 5.7 years ago
United States

Hello Laurent, 

I am sorry it has taken so long to respond. I had some computer difficulties and have been moving. I have had to switch computers. This is my new sessionInfo() output.

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] synapter_1.10.0     MSnbase_1.16.2      ProtGenerics_1.0.0 
[4] BiocParallel_1.2.21 mzR_2.2.1           Rcpp_0.12.0        
[7] Biobase_2.28.0      BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2    XVector_0.8.0         BiocInstaller_1.18.4 
 [4] futile.logger_1.4.1   plyr_1.8.3            iterators_1.0.7      
 [7] futile.options_1.0.0  tools_3.2.2           zlibbioc_1.14.0      
[10] MALDIquant_1.12       digest_0.6.8          preprocessCore_1.30.0
[13] gtable_0.1.2          lattice_0.20-33       foreach_1.4.2        
[16] proto_0.3-10          hwriter_1.3.2         knitr_1.11           
[19] stringr_1.0.0         Biostrings_2.36.4     S4Vectors_0.6.5      
[22] IRanges_2.2.7         multtest_2.24.0       stats4_3.2.2         
[25] grid_3.2.2            qvalue_2.0.0          impute_1.42.0        
[28] survival_2.38-3       XML_3.98-1.3          limma_3.24.15        
[31] cleaver_1.6.0         ggplot2_1.0.1         reshape2_1.4.1       
[34] lambda.r_1.1.7        magrittr_1.5          splines_3.2.2        
[37] scales_0.3.0          pcaMethods_1.58.0     codetools_0.2-14     
[40] MASS_7.3-44           mzID_1.6.0            colorspace_1.2-6     
[43] stringi_0.5-5         affy_1.46.1           munsell_0.4.2        
[46] doParallel_1.0.8      vsn_3.36.0            affyio_1.36.0   

 

This is my colnames(obj$MatchedEMRTs) output

 [1] "protein.key"                         
  [2] "protein.Entry"                       
  [3] "protein.Accession"                   
  [4] "protein.Description"                 
  [5] "protein.dataBaseType"                
  [6] "protein.score"                       
  [7] "protein.falsePositiveRate"           
  [8] "protein.avgMass"                     
  [9] "protein.MatchedProducts"             
 [10] "protein.matchedPeptides"             
 [11] "protein.digestPeps"                  
 [12] "protein.seqCover..."                 
 [13] "protein.MatchedPeptideIntenSum"      
 [14] "protein.top3MatchedPeptideIntenSum"  
 [15] "protein.MatchedProductIntenSum"      
 [16] "protein.fmolOnColumn"                
 [17] "protein.ngramOnColumn"               
 [18] "protein.AutoCurate"                  
 [19] "protein.Key_ForHomologs"             
 [20] "protein.SumForTotalProteins"         
 [21] "peptide.Rank"                        
 [22] "peptide.Pass"                        
 [23] "peptide.matchType"                   
 [24] "peptide.modification"                
 [25] "peptide.mhp"                         
 [26] "peptide.seq"                         
 [27] "peptide.OriginatingSeq"              
 [28] "peptide.seqStart"                    
 [29] "peptide.seqLength"                   
 [30] "peptide.pI"                          
 [31] "peptide.componentID"                 
 [32] "peptide.MatchedProducts"             
 [33] "peptide.UniqueProducts"              
 [34] "peptide.ConsectiveMatchedProducts"   
 [35] "peptide.ComplementaryMatchedProducts"
 [36] "peptide.rawScore"                    
 [37] "peptide.score"                       
 [38] "peptide..X..P.Bond"                  
 [39] "peptide.MatchedProductsSumInten"     
 [40] "peptide.MatchedProductsTheoretical"  
 [41] "peptide.MatchedProductsString"       
 [42] "peptide.ModelRT"                     
 [43] "peptide.Volume"                      
 [44] "peptide.CSA"                         
 [45] "peptide.ModelDrift"                  
 [46] "peptide.RelIntensity"                
 [47] "peptide.AutoCurate"                  
 [48] "precursor.leID.ident"                
 [49] "precursor.mhp"                       
 [50] "precursor.mhpCal"                    
 [51] "precursor.retT"                      
 [52] "precursor.inten"                     
 [53] "precursor.calcInten"                 
 [54] "precursor.charge"                    
 [55] "precursor.z"                         
 [56] "precursor.mz"                        
 [57] "precursor.fwhm"                      
 [58] "precursor.liftOffRT"                 
 [59] "precursor.infUpRT"                   
 [60] "precursor.infDownRT"                 
 [61] "precursor.touchDownRT"               
 [62] "prec.rmsFWHMDelta"                   
 [63] "peptidePrecursor.deltaMhpPPM"        
 [64] "errorppm"                            
 [65] "pval"                                
 [66] "qval"                                
 [67] "BH"                                  
 [68] "Bonferroni"                          
 [69] "predictedRt"                         
 [70] "sdRt"                                
 [71] "Function"                            
 [72] "spectrumID"                          
 [73] "isBinned"                            
 [74] "rt_min"                              
 [75] "rtErr"                               
 [76] "mwHPlus"                             
 [77] "errPPM"                              
 [78] "charge"                              
 [79] "Intensity"                           
 [80] "Counts"                              
 [81] "errCounts"                           
 [82] "pep_numIons"                         
 [83] "clusterID"                           
 [84] "charge_numIons"                      
 [85] "isFid"                               
 [86] "ion_ID"                              
 [87] "ion_z"                               
 [88] "ion_iso"                             
 [89] "charge_mwHPlus"                      
 [90] "ion_rt"                              
 [91] "ion_rtSd"                            
 [92] "ion_fwhm"                            
 [93] "ion_area"                            
 [94] "ion_counts"                          
 [95] "ion_intenSD"                         
 [96] "ion_m_z"                             
 [97] "ion_m_zUncal"                        
 [98] "ion_m_zSD"                           
 [99] "ion_satFlag"                         
[100] "ion_deltaPPM"                        
[101] "ion_deltaT"                          
[102] "ion_clusterDeltaPPM"                 
[103] "ion_ratio12C"                        
[104] "Model"                               
[105] "ratioToModel"                        
[106] "matched.quant.spectrumIDs"           
[107] "precursor.leID.quant"                
[108] "idSource"                            

Again, I am very sorry for the delayed response. 

Thanks, 

Diana

 

 

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@dianaschreier-8621
Last seen 5.7 years ago
United States

That's great. I look forward to using it. 

 

Thank you for your help. I greatly appreciate it.

 

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@dianaschreier-8621
Last seen 5.7 years ago
United States

Hi Laurent, 

​I have been checking the link you provided earlier for the updated 1.11.1 version to become available, but I have not seen it. Am I looking in the wrong location?

 

Thank you, 

Diana

 

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I don't see any commits to the devel branch since April 16...

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Sorry, I forgot to commit to svn. This is done now, but in the meantime, you can get the source tar ball here. Let me know if you need any help. Sorry again for the inconvenience.

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