Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto1.1k
Reputation:
1,130
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Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
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Google Scholar Page
Last seen:
17 hours ago
Joined:
11 years, 10 months ago
Email:
l************@gmail.com

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 • 249 results • page 1 of 25 • next >
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DataFrame after splitting and back
... I have the following `DataFrame` ``` > k <- sample(3, 10, replace = TRUE) > df <- DataFrame(k = k, + x = round(rnorm(length(k)), 2), + y = seq_len(length(k)), + z = sample(LETTERS, length(k), replace = TRUE), + ir = IRange ...
s4vectors dataframe written 22 hours ago by Laurent Gatto1.1k • updated 20 hours ago by Michael Lawrence11k
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Comment: C: Error when loading MSnbase package "object 'vI' not found"
... Weird... Could you try to `remove.packages("MSnbase")` and re-install it again. I wonder if this might not be related to packages and their dependencies being installed in different libraries. What's your output of `.libPaths()`? ...
written 28 days ago by Laurent Gatto1.1k
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Answer: A: Error when loading MSnbase package "object 'vI' not found"
... Strange, and unlikely to be an `MSnbase` issue. Could you 1. restart R altogether 2. re-install with `BiocManager::install("MSnbase")` 3. load `library("MSnbase")` If the above fails, could you provide the end of the installation output. ...
written 28 days ago by Laurent Gatto1.1k
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Answer: A: Comparative proteome analysis of two different species
... What kind of quantitation are you planning to use? It will be a label-free approach, but depending on whether you want to use spectral counting or M1 label-free, you will need different software. You will also need to search your data against a protein database using a search engine (Mascot, MSGF+, ...
written 29 days ago by Laurent Gatto1.1k
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Answer: A: Errors installing "shinyTANDEM" package
... Have you tried to install the package with ``` BiocManager::install("shinyTANDEM") ``` That would certainly help. ...
written 5 weeks ago by Laurent Gatto1.1k
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Comment: C: Problems with cholesky decomposition in pRoloc package
... Thank you. I will need to check if it was backported correctly - will do that at work this morning. In the meantime, you could try to install the latest version with `BiocManager::install("lgatto/pRoloc")`. ...
written 5 weeks ago by Laurent Gatto1.1k
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Answer: A: Problems with cholesky decomposition in pRoloc package
... Could you provide the output of `sessionInfo` please. This was addressed end of last year, which should be available in the latest devel (version 1.23.1). ...
written 6 weeks ago by Laurent Gatto1.1k
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Answer: A: Errors installing mzR package
... The `mzR` package is missing. The lines that tried to installed `RforProteomics` and `MSnbase` must have failed, as both depend on `mzR`. To install `mzR` you will first have to install a system dependency, `ncdf4`, using your package manager. On ubuntu/debian, it should be `sudo apt install libn ...
written 6 weeks ago by Laurent Gatto1.1k
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Job: Full time and permanent research logistician in Bioinformatics
... UCLouvain is recruiting a Research Logistician in Bioinformatics - full-time with a permanent contract - for the Louvain Institute of Biomolecular Science and Technology (LIBST) - in Louvain-la-Neuve **Context and organization** The Research logistician in bioinformatics will be based in the Louv ...
proteomics job bioinformatician transcriptomics written 7 weeks ago by Laurent Gatto1.1k
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Comment: C: Protein quantification by MSnbase package
... I think you will have to start from mzID files to use `MSnID`. As for spectral counting using `MSnbase`, I would that you would want to count the reliable PSMs (based on their q-value) that have been associated to a protein group. So the `fcol` argument should probably be `Accession`. ...
written 8 weeks ago by Laurent Gatto1.1k

Latest awards to Laurent Gatto

Scholar 10 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Does OnDiskMSnExp rewrite original data
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Selecting genes based on expressional variance
Scholar 11 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 11 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 22 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 22 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Scholar 22 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 22 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 23 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
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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Scholar 3.5 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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