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fbreitwieser / isobar

isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data
https://bioconductor.org/packages/release/bioc/html/isobar.html
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"object 'spectrumId' not found" error while loading idspectra file #1

Closed pvannierop closed 11 years ago

pvannierop commented 11 years ago

Hello,

With my firsts steps with Isobar (installed through Bioconductor) I run into problems when loading my spectra info from file. The command issued is:

ib = readIBSpectra("iTRAQ8plexSpectra",id.file="set1_merge_mod_head.ibspectra.csv")

The error is:

reading set1_merge_mod_head.ibspectra.csv
merging identifications
Error in .nextMethod(.Object, ...) : object 'spectrumId' not found

This is the first line of the "set1_merge_mod_head.ibspectra.csv" file, that displays the same error as the full text file that contains ~20000 lines:

"spectrum"  "accession" "peptide"   "X113_mass" "X114_mass" "X115_mass" "X116_mass" "X117_mass" "X118_mass" "X119_mass" "X120_mass" "X121_mass" "X113_ions" "X114_ions" "X115_ions" "X116_ions" "X117_ions" "X118_ions" "X119_ions" "X120_ions" "X121_ions" "modif"
"1" 371536  "spP97445CAC1A_MOUSE"   "ESEPQQR"   113.097336  114.105591  115.098007  116.100708  117.108368  118.104668  119.104736  120.09726   121.118034  2542.211    3916.099    3411.615    3075.347    2359.421    4534.202    2088.24 244.25  2602.13 " "

As far as I can see, I have no errors in my file, but I cannot make my first steps in the use of Isobar. Any help would be greatly appreciated.

Pim van Nierop CNCR, VU University, Amsterdam

pvannierop commented 11 years ago

UPDATE: Since I am on version 1.4.0 now and I see that the most recent version here on GitHub is 1.5.2. I reran the steps as shown above and there was not problem anymore. So please be aware that the version as advertised on Bioconductor is out of date. I did however get the following warning when reading in the the full file:

Warning messages:
1: In .local(from, proteinInfo) :
  start.pos not in supplied data.frame, setting to NA
2: In .get.quant.elems(assayDataElements, data.ions, data.mass, identifications[,  :
  19970 spectra could not be mapped from quant to id: 371536;371537;371552;371553;371554;371558;371563;371572;371578;371579

In fact, this mapping problem, that I do not know where it originates from, applies to all spectrum annotations in the file.

head(ib)

Gives:

iTRAQ8plexSpectra (storageMode: lockedEnvironment)
assayData: 1 features, 8 samples 
  element names: ions, mass 
protocolData: none
phenoData: none
featureData
  featureNames: 371536
  fvarLabels: spectrum peptide ... use.for.quant (5 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
1  spectra
ProteinGroup object
    8049 peptides are detected
    2252 protein groups with specific peptides
fbreitwieser commented 11 years ago

Thank you for the bug report. I fixed the Bioconductor version. I do recommend using the Github version. Bioconductor does not like that new features or functions are introduced in the release versions, but only in a development branch. This will be in the release version with the next Bioc release.

For the second issue: Please try again with the newest version from the ptm branch. If it does not work, please provide the readIBSpectra command you use and attach small sample file (~50 lines).