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

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

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

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

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

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

Thank you for your help. I greatly appreciate it.

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