Moderator: Laurent Gatto

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Laurent Gatto1.2k
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Belgium
Website:
http://lgatto.github.io/
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lgatt0
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12 years, 3 months ago
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I am a Professor of Bioinformatics at the de Duve Institute, at the UCLouvain, Belgium. I am an avid open research advocate and make every possible effort to make my research reproducible and openly available. I am a Software Sustainability Institute fellow and a Data and Software Carpentry instructor. Since 2010, I have been focusing on various aspects of quantitative and spatial proteomics, developing new methods and implementing computational tools with a strong emphasis on rigorous and reproducible data analysis.

Posts by Laurent Gatto

<prev • 264 results • page 1 of 27 • next >
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Comment: C: Writing a loop through multiple fasta files and named files (is it possible with
... You could try to run MSGF+ natively. I have no idea if running it through the `MSGFplus` package has an actual overhead in term of memory, but worth a try. If this fails, you'll probably need a computer with more memory. ...
written 1 day ago by Laurent Gatto1.2k
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Comment: C: Writing a loop through multiple fasta files and named files (is it possible with
... Iterating over multiple fasta is technically possible, but I am not sure it is valid. When identifying your peptides, a identification probability is computed that takes into account the risk of calling wrong peptide spectrum matches. That probability depends on the search space, i.e. the size of yo ...
written 1 day ago by Laurent Gatto1.2k
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Answer: A: European Bioconductor meeting 2019, 9 - 10 December in Brussels, Belgium
... Flashlight and poster abstract submissions are now open at http://eurobioc2019.bioconductor.org/registration ...
written 20 days ago by Laurent Gatto1.2k
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News: European Bioconductor meeting 2019, 9 - 10 December in Brussels, Belgium
... The European Bioconductor meeting is aimed at biologists, bioinformaticians, statisticians, programmers and software engineers who use or contribute to the Bioconductor project, or are interested in using Bioconductor. The goals are to: - foster the exchange of technical expertise - keep contribu ...
news conference eurobioc written 20 days ago by Laurent Gatto1.2k
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Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
... A position for a PhD student or post-doctoral research is open in the group of Prof Laurent Gatto at the UCLouvain (Brussels, Belgium) in collaboration with Prof Vince Carey at Harvard University (Boston, MA, USA) to develop the necessary infrastructure and statistical software to integrate genomic, ...
proteomics job software genomics transcriptomics written 21 days ago by Laurent Gatto1.2k
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Comment: C: runInfo returns startTimeStamp -infinity
... The only advise I can give you is to download the RAW files and check in there and/or reconvert them to mzML. Other then that, you can try to contact the authors. ...
written 6 weeks ago by Laurent Gatto1.2k
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Comment: C: runInfo returns startTimeStamp -infinity
... I don't think there is from that mzML file. You might have to check in the raw binary file, or try to convert it again and see if it was missed out in the first place. ...
written 6 weeks ago by Laurent Gatto1.2k
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Answer: A: runInfo returns startTimeStamp -infinity
... I think you are missing some bits of code in your example - it probably should be ``` ms <- openMSfile('path/to/file.mzML') info <- runInfo(ms) ms$startTimeStamp ``` The reason you read `"-infinity"` is probably because that's what is encoded in your `mzML` file. You can check for yourself in ...
written 6 weeks ago by Laurent Gatto1.2k
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Answer: A: pRoloc - phenoDisco - issue with example
... Thank you very much for the bug report. The issue wasn't in `phenoDisco` itself (which used the appropriate feature variable), but a helper function (`anyUnknown`) that performed some test and that didn't get the user's `fcol` passed along. The issue is fixed in version 1.25.2 that is available im ...
written 9 weeks ago by Laurent Gatto1.2k
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Answer: A: Extracting Data from MSn experiment data ("OnDiskMSnExp")
... You can use the respective accessors to extract these information from the object. Below, I use the `serine` object created in the [`MSnbase` *centroiding* vignette](http://lgatto.github.io/MSnbase/articles/v03-MSnbase-centroiding.html): ``` > str(head(intensity(serine))) List of 6 $ F1.S628: n ...
written 11 weeks ago by Laurent Gatto1.2k

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