Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto1.2k
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Location:
Belgium
Website:
http://lgatto.github.io/
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lgatt0
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Google Scholar Page
Last seen:
1 day ago
Joined:
12 years, 1 month 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 • 256 results • page 1 of 26 • next >
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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 12 days 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 23 days ago by Laurent Gatto1.2k
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Answer: A: Access list of rtime/intensity values from chromatograms object from MSnbase
... Below, I have the `chrs` object as created in `?Chromatograms`. It is possible to extract the retention time and intensities from individual chromatogram composing the `Chromatograms` with `rtime` and `intensity`: ``` > chrs Chromatograms with 2 rows and 2 columns 1 ...
written 23 days ago by Laurent Gatto1.2k
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Comment: C: MSnbase addIdentificationData problem
... Something along those lines yes. ...
written 8 weeks ago by Laurent Gatto1.2k
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Answer: A: MSnbase addIdentificationData problem
... The previous post to refer to is different than you issue. In your case, unfortunately, the `addIdentificationData` will not work as it expects to find information that it can't find when reading data from an `mgf` file. This code was written for the more complete `mzML` format in mind. What you ca ...
written 9 weeks ago by Laurent Gatto1.2k
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Comment: C: MSnbase addIdentificationData problem
... Could you point me to the previous occurrence of this issue - it might help understanding what to underlying problem it. Also, could you share the data for debugging? ...
written 9 weeks ago by Laurent Gatto1.2k
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Answer: A: MSnbase extracting individual spectrum based on precursor ion m/z
... This is most likely due to the fact that the precursor M/Z isn't exactly 808.5253. 808.5253 is probably a rounded up value that is shown as part of showing the spectrum object, and `==` returns `TRUE` when the two values are exactly identical. You would need to check the exact value of the M/Z value ...
written 10 weeks ago by Laurent Gatto1.2k
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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 3 months ago by Laurent Gatto1.2k • updated 3 months 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 4 months ago by Laurent Gatto1.2k
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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 4 months ago by Laurent Gatto1.2k

Latest awards to Laurent Gatto

Scholar 23 days ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 7 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 7 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 14 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Does OnDiskMSnExp rewrite original data
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Selecting genes based on expressional variance
Scholar 15 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 15 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 2.2 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.2 years ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
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Scholar 2.2 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 3.4 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
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