User: Sebastian Gibb

Reputation:
80
Status:
Trusted
Location:
Germany
Website:
http://www.sebastiangi...
Scholar ID:
Google Scholar Page
Last seen:
9 months, 1 week ago
Joined:
4 years, 9 months ago
Email:
m***@sebastiangibb.de

Posts by Sebastian Gibb

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Writing a loop to clean up protein names
... You are right. Your solution will be even twice as fast as the gsub if you use fixed=TRUE and vapply: z <- rep(c( "tr|A1A02DLI66|A0A02DLI66_MYTGA", "tr|B2XC03|B1XC03_ECODH HU, DNA-binding transcriptional regulator", "tr|A10UF05|A9UF05_HUMAN BCR/ABL fusion protein isoform Y3" ), 5e3) ...
written 9 months ago by Sebastian Gibb80
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Answer: A: Writing a loop to clean up protein names
... This is a typical fasta header (see the following link for a full explanation: https://www.uniprot.org/help/fasta-headers). While using strsplit is easy to understand it requires a loop (or *apply) to access the AccessionNumber/UnqiueIdentifier. You could use gsub with a different pattern to use a v ...
written 9 months ago by Sebastian Gibb80
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Answer: A: Extract whether list element is MS1 or MS2 from mzR::peaks() output
... You have to access the header information (?header) first. Subsequently you could subset peaks() (second argument, which is unfortunately missing in the Usage section of the manual page but present in the Details. (I opened an issue on github: https://github.com/sneumann/mzR/issues/134)): library ...
written 21 months ago by Sebastian Gibb80
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Comment: C: Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to bui
... > Sure...the fasta file is mouse uniprotproteome(~50,000 entries). Ok, I can download it myself. I assume this one: http://www.uniprot.org/proteomes/UP000000589 > The mzid file is 50 MB. I was testing the the first 10 entries in the Proteins database. How shouldI send then to you. Can you upl ...
written 3.4 years ago by Sebastian Gibb80
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Comment: C: Pbase: AddIdentificationData. How can I use MSnId objects (filtered psm) to bui
... The error is correct. That happens because your `aa` slot is not in alphabetical order. Maybe that's a bug. Could you send me the fasta and the mzID file? ...
written 3.4 years ago by Sebastian Gibb80
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Comment: C: Converting Synapter object output into a MSnbase-compatible object
... 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") ...
written 3.8 years ago by Sebastian Gibb80
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Comment: C: problem with Pbase mapping vignette
... First, I am one of the maintainers and that's why I am knowing that we changed the `p` object in the past sometimes. Next there is a line `Created` in the output with an outdated date: `Created : Wed Jul 16 02:58:33 2014`. ...
written 3.9 years ago by Sebastian Gibb80
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Answer: A: problem with Pbase mapping vignette
... Indeed it seems you are using an old version of `Pbase`. What does `sessionInfo()` say? Did you try to update `Pbase` using `source("http://bioconductor.org/biocLite.R"); biocLite("Pbase")`? ...
written 3.9 years ago by Sebastian Gibb80
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Answer: A: Load data in Synapter
... There are several ways to save and load an R object. You could use 'save' and 'load' as you tried. 'load' will add the object to your global environment (and return the object name invisible). That's why your loading fails. You overwrite the real object by its name. Try just: 'load("yourfile")' inst ...
written 4.6 years ago by Sebastian Gibb80
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Answer: A: Synapter - makeMaster() and synergise() functions warnings/fails
... As described here we recognized the problem some time ago. Because of that I assume that there is no problem with the IDs but with the corresponding intensities. It sounds suprising but in some cases the intensity values in a final_peptide file and its corresponding Pep3D file don't match. A simple ...
written 4.6 years ago by Sebastian Gibb80 • updated 4.6 years ago by Laurent Gatto1.1k

Latest awards to Sebastian Gibb

Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: problem with Pbase mapping vignette
Scholar 3.9 years ago, created an answer that has been accepted. For A: problem with Pbase mapping vignette

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