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Question: Converting Synapter object output into a MSnbase-compatible object
0
gravatar for diana.schreier
2.3 years ago by
United States
diana.schreier0 wrote:

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

ADD COMMENTlink modified 2.2 years ago • written 2.3 years ago by diana.schreier0
1
gravatar for Laurent Gatto
2.2 years ago by
Laurent Gatto840
United Kingdom
Laurent Gatto840 wrote:

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

 

 

 

 

ADD COMMENTlink written 2.2 years ago by Laurent Gatto840
1
gravatar for diana.schreier
2.2 years ago by
United States
diana.schreier0 wrote:

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

 

 

 

ADD COMMENTlink written 2.2 years ago by diana.schreier0
2

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")

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Sebastian Gibb80

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

ADD REPLYlink written 2.2 years ago by diana.schreier0

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

ADD REPLYlink written 2.2 years ago by Laurent Gatto840
0
gravatar for Laurent Gatto
2.3 years ago by
Laurent Gatto840
United Kingdom
Laurent Gatto840 wrote:
>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.
ADD COMMENTlink written 2.3 years ago by Laurent Gatto840
0
gravatar for Laurent Gatto
2.3 years ago by
Laurent Gatto840
United Kingdom
Laurent Gatto840 wrote:
>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.
ADD COMMENTlink written 2.3 years ago by Laurent Gatto840
0
gravatar for diana.schreier
2.3 years ago by
United States
diana.schreier0 wrote:

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

ADD COMMENTlink written 2.3 years ago by diana.schreier0

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.

ADD REPLYlink written 2.3 years ago by Laurent Gatto840
0
gravatar for diana.schreier
2.2 years ago by
United States
diana.schreier0 wrote:

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

 

 

ADD COMMENTlink written 2.2 years ago by diana.schreier0
0
gravatar for diana.schreier
2.2 years ago by
United States
diana.schreier0 wrote:

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

 

Thank you for your help. I greatly appreciate it.

 

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by diana.schreier0
0
gravatar for diana.schreier
2.2 years ago by
United States
diana.schreier0 wrote:

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

 

ADD COMMENTlink written 2.2 years ago by diana.schreier0

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

ADD REPLYlink written 2.2 years ago by Dan Tenenbaum ♦♦ 8.2k

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.

ADD REPLYlink written 2.2 years ago by Laurent Gatto840
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