Moderator: Laurent Gatto

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Laurent Gatto1.0k
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United Kingdom
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http://lgatto.github.io/
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lgatt0
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Last seen:
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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

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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
... The Computational Biology (CBIO) unit at the de Duve Institute in Brussels, Belgium, seeks to appoint a full time research software engineer. The successful candidate will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of bio ...
job bioconductor teaching software engineer written 1 hour ago by Laurent Gatto1.0k
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Comment: C: msmsTests, NA values in test.results output
... It would probably be helpful to provide code, detailed output and possibly example data. Also, don't forget to add the output of `sessionInfo()`. ...
written 16 hours ago by Laurent Gatto1.0k
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Comment: C: msmsTests, NA values in test.results output
... Do you have any `NA` values in your original count data by any chance? ...
written 1 day ago by Laurent Gatto1.0k
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Answer: A: quantify() method for MSnExp to MSnSet for MS1 level data only
... In your question, you mention that the data was supposed to be MS/MS - does that mean to you were supposed to quantify in MS2, or only that the MS2 for identification is missing? Assuming it the latter, quantify() doesn't work (yet) for MS1 quantitation. You could look at the rawDiag package or xcms ...
written 4 weeks ago by Laurent Gatto1.0k
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Answer: A: Does OnDiskMSnExp rewrite original data
... Hi Goh, No, your original data isn't modified at all. The only way to modify raw data on disk is to write it explicitly to a file using writeMSData. Note however that in your example, the raw data object raw_data, once created, isn't modified at all, as you use xdata to adjust retention time - prob ...
written 8 weeks ago by Laurent Gatto1.0k
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Comment: C: mZR: access "parentFile" tag
... Yes, it's exactly something like that I was thinking of. Note that there's the fileNames function to extract the file name of the mz[X]ML file, but that can be different than the original file. > library("MSnbase") > ms <- readMSData("file.mzML", mode = "onDisk") > (f <- fileNames(m ...
written 4 months ago by Laurent Gatto1.0k
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Comment: C: mZR: access "parentFile" tag
... I was rather thinking about accessing the relevant information by extracting it from the XML file directly (using the `XML` or `xml2` packages), rather than converting it to a database. The latter is an interesting approach which has advantages, but is a bit too heavy-handed to extract a single tag. ...
written 4 months ago by Laurent Gatto1.0k
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Answer: A: mZR: access "parentFile" tag
... No, I don't think so. In addition, it looks like that tag is different in mzML files, which we tend to develop for now. This is something that we could consider adding and shouldn't be too difficult using xml2 - PR on github welcome.   ...
written 4 months ago by Laurent Gatto1.0k
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Answer: A: Thermo Xcalibur RAW data to MGF
... The short answer is no, because to access (and this convert) proprietary Thermo raw data, you need to their libraries that are only available on Windows. That would mean that an R package would need to (i) incorporate these proprietary binary Thermo libraries and (ii) only be available on Windows. Y ...
written 5 months ago by Laurent Gatto1.0k
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Answer: A: Label free quantification post FDR calculation for MS/MS Proteomics
... If you want to do spectral counting, you can proceed from an MSnID workflow to MSnbase by converting your MSnID objects to MSnSet data using the as method, as documented at the end of the MSnID vignette. You could then combine multiple MSnSet data object (for different samples) using the combine met ...
written 5 months ago by Laurent Gatto1.0k

Latest awards to Laurent Gatto

Scholar 4 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Does OnDiskMSnExp rewrite original data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Selecting genes based on expressional variance
Scholar 5 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 5 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 16 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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Scholar 16 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Scholar 16 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 16 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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Scholar 2.5 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.5 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 2.6 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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Scholar 3.0 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 3.0 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
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