Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto820
Reputation:
820
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
1 week, 4 days ago
Joined:
10 years, 3 months ago
Email:
l****@cam.ac.uk

Laurent Gatto is a senior research associate in the Department of Biochemistry, University of Cambridge and a visiting scientist in the PRIDE team at the EBI. He graduated in Biology from the Free University of Brussels, Belgium, and subsequently earned his PhD in Evolutionary Biology. He pursued his education at the University of Namur studying Computer Science before working in industry on genetic and transcriptomic data analysis. In January 2010, he joined the Cambridge Centre for Proteomics to work on quantitative and organelle proteomics and. In August 2013, he established the Computational Proteomics Unit in the Cambridge System Biology Centre.

Posts by Laurent Gatto

<prev • 181 results • page 1 of 19 • next >
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Comment: C: mzR library issue
... [First name is Laurent] Is this in a new session, i.e. you restarted R? If so, do you have an .Rprofile files that loads some packages automatically? To avoid anything like that, could you start R in a terminal with R --vanilla, then type the following: ls() sessionInfo() library("Rccp") library( ...
written 29 days ago by Laurent Gatto820
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Answer: A: mzR library issue
... Could you try the following in a new R session: library("Rcpp") library("mzR") sesssionInfo() and, if you encounter any errors, could you provide the full output of the session, including the output of sessionInfo(). ...
written 4 weeks ago by Laurent Gatto820
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Answer: A: Query regarding Prostar
... You could try to load that spreadsheet data directly as an MSnSet using readMSnSet2 and then proceed using Prostar (I believe they support them). ...
written 8 weeks ago by Laurent Gatto820
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Comment: C: Missing value imputation
... Yes, that seems reasonable. I am unsure about using the peptide average rather than another suitable MAR method (as this will artificially minimise the variability for that peptide and the statistical tests might then be too optimistic), but I guess by trying and inspecting results, you will see. ...
written 8 weeks ago by Laurent Gatto820
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Answer: A: Missing value imputation
... I don't think it matters, as long as you wouldn't use a zero imputation for MNAR. However, as you use TMT tags, one would expect your missing values to be the results of absent peptides, rather than the MS missing features, because samples were combined. If it is a typical shotgun experiment, one w ...
written 8 weeks ago by Laurent Gatto820
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Comment: C: qcmetrics package and longitudinal qc data
... Peptide sequences are not available when one only calls readMSData[2], as this function only accesses data from the raw files. But it is possible to add the identifiction data to the raw MSnExp objects using addIdentificationData. Then, the identification results, including the peptide sequences, wi ...
written 8 weeks ago by Laurent Gatto820
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Comment: C: Post-doctoral mass spectrometry and proteomics bioinformatician (updated)
... This position hasn't been filled and is being re-advertised. ...
written 9 weeks ago by Laurent Gatto820
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Comment: C: qcmetrics package and longitudinal qc data
... Hi Eralp, The function above looks sensible. I would suggest you use readMSData2 as it will be much faster (it won't read the raw data into memory), but you'll need to make sure you also define the MS level that you wish to read (by default, it reads all levels). Also, you can probably drop the c() ...
written 9 weeks ago by Laurent Gatto820
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Answer: A: Problem in installing bioconductor
... The message you show looks good - this is exactly what you are supposed to see. Now, you need to decide what package to use depending on the type of data you have and analysis you want to do.     ...
written 10 weeks ago by Laurent Gatto820
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Answer: A: qcmetrics package and longitudinal qc data
... Your question is not clear to me. Could you clarify what you are trying to do and/or answer the following questions. Are you replicating the example for raw MS data shown in the qcmetrics vignette, or are you creating you own QcMetric objects? What is your input format, and what operability with ...
written 10 weeks ago by Laurent Gatto820

Latest awards to Laurent Gatto

Scholar 3 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 3 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 4 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 17 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 17 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 19 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 23 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 23 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 23 months ago, created 100 posts.
Supporter 3.0 years ago, voted at least 25 times.
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