Error in `$<-.data.frame`(`*tmp*`, page, value = 1) : replacement has 1 row, data has 0 [UTF-8 BOM issue]

[GeorgTascher]

Dear Chris,

I recently started to use a newer version of MaxQuant (2.4.0.0) and PTXQC crashes directly:

Starting to work on PAR: MQ Parameters ... Error in $<-.data.frame(*tmp*, page, value = 1) : replacement has 1 row, data has 0

I use PTXQC v1.0.14 on a Win 2012 server using R Studio 2022.02.2 with running R 3.6.3 (a bit old, I know....) I didnt try other versions than my "stable" MaxQuant release (1.6.17.0), so I dont know if this problem was introduced already some MQ-versions before or only in this version. What I can say is that the "parameters.txt" is different between the two versions....

Is this problem known?

Cheers and thanks for this REALLY useful tool! Georg

[cbielow]

Hi Georg,

can you provide the full txt folder?! This would make it much easier to identify the problem.

[GeorgTascher]

Hi Chris, Thank you for your prompt reply! Sure, sorry, here is the link to WeTransfer, folder was to big to upload it here: https://we.tl/t-d9KDmKO9Wz

[cbielow]

Hi Georg,

the problem here originates from a new encoding which MaxQuant uses for its txt files. They now start each file with a byte-order mark (BOM), which trips up the R function for reading text files. This is especially weird, since the encoding is UTF-8, and using a BOM for UTF-8 is not recommended.

Well, the problem is fixed in the latest PTX-QC release (1.0.16), which you can get from Github (see installation instructions on main page) or wait a few days until the CRAN release has trickled through.

Thanks for reporting the problem!

[GeorgTascher]

Hi Chris,

lieber spät als nie...vielen Dank fürs troubleshooting, funktioniert jetzt wieder einwandfrei!

Viele Grüße Georg

Dr. Georg Tascher

Team Leader Quantitative Proteomics Unit Institut für Biochemie II

Gustav Embden-Zentrum der Biochemie Goethe-Universität Frankfurt - Fachbereich Medizin

Universitätsklinikum - Gebäude 75 (lab) & 69 (office) Theodor-Stern-Kai 7 60590 Frankfurt am Main

Tel : +49 (0)69 6301 84757 Fax : +49 (0)69 6301 5577 @. @.> http://www.biochem2.de http://www.biochem2.de/

On 17. May 2023, at 16:18, Chris Bielow @.***> wrote:

Hi Georg,

the problem here originates from a new encoding which MaxQuant uses for its txt files. They now start each file with a byte-order mark (BOM) https://en.wikipedia.org/wiki/Byte_order_mark, which trips up the R function for reading text files. This is especially weird, since the encoding is UTF-8, and using a BOM for UTF-8 is not recommended.

Well, the problem is fixed in the latest PTX-QC release (1.0.16), which you can get from Github (see installation instructions on main page) or wait a few days until the CRAN release has trickled through.

Thanks for reporting the problem!

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[cbielow]

Glad to hear it works! Thanks again for reporting!