No filename when adding id data

[lgatto]

When loading mzid files that do not return the id filename as part of the data.frame column, addIdentificationData throws the following error via utils.addSingleIdentificationDataFile:

Error in basename(id$spectrumFile) : a character vector argument expected

See https://groups.google.com/forum/#!topic/rbioc-sig-proteomics/na-dMumFgAU

There should be another or a second mechanism to handle this situations.

[lgatto]

The code accommodate such cases has been written, the real issue might lie somewhere else.

The bug report comes from a user that uses X!TANDEM, that uses mgf files as input, rather than directly mz[X]ML. The current changes in the code will detect and warn that there is a discrepancy between what was used to produce the mzid file (i.e. foo.mgf) and what the MSnExp was created with (i.e. foo.mzML). But I still have to figure out if it remains possible to do the actual matching between spectra in the MSnExp and mzid in such situations (or even in cases where both stem from foo.mgf).

[Xabiermm1]

I think this could works , with iTRAQ 4

Its the default input.xml file, for xtandem

2014-10-17 10:49 GMT+02:00 Laurent Gatto notifications@github.com:

The code accommodate such cases has been written, the real issue might lie
somewhere else.

The bug report comes from a user that uses X!TANDEM, that uses mgf files
as input, rather than directly mz[X]ML. The current changes in the code
will detect and warn that there is a discrepancy between what was used to
produce the mzid file (i.e. foo.mgf) and what the MSnExp was created with
(i.e. foo.mzML). But I still have to figure out if it remains possible to
do the actual matching between spectra in the MSnExp and mzid in such
situations (or even in cases where both stem from foo.mgf).

—
Reply to this email directly or view it on GitHub
#39 (comment).

[sgibb]

According to the mzIdentML specification there must be a <SpectraData> element (maybe it is worth to ask for a fix upstream?). As fallback it should be sufficient to show a warning and compare both filenames. In most cases the filenames should be the same.

The current changes in the code will detect and warn that there is a discrepancy between what was used to produce the mzid file (i.e. foo.mgf) and what the MSnExp was created with (i.e. foo.mzML).

@lgatto Did you already push these changes?

[lgatto]

Just pushed now.

The issue is not <SpectraData> in mzid files, but the absence thereof (and any other well defined annotation) if the mzid was generated using an mgf file, which is very poor in meta-data. I will need to run some tests to figure out, but I have the feeling that such cases will have to be dealt with manually by the user.

[mdkasoji]

Hi,

From reading the thread, it seems that you have fixed this issue? I am still receiving this error message. My raw data input files were mzXML (converted from .raw to mzXML) using proteowizard and the mzIdent files were generated from Mascot.

Any suggestions on how to get past this error?

Here is my code:

files=dir("/Users/kasojimd/Projects/ccrifx-541/Raw2mzXML",full.names=T,patter="mzXML")

rawdata=readMSData(files)

identFile=list.files(pattern=".mzid$")

msexp <- addIdentificationData(rawdata, filenames = identFile, verbose = FALSE)
Error in basename(id$spectrumFile) : a character vector argument expected

Any suggestions will be appreciated!

Thanks!

[lgatto]

Please do not cross-post. See your post on the Bioc support site for an answer.