Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto880
Reputation:
880
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
10 years, 7 months ago
Email:
l****@cam.ac.uk

I am a Senior Research Associate in the Department of Biochemistry at the University of Cambridge. 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 and a founding member of OpenConCam, our local OpenCon group. I moved to Cambridge, UK, in January 2010 to work in the Cambridge Centre for Proteomics 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. I am also a visiting scientist in the PRIDE team at the European Bioinformatics Institute, and an affiliate teaching staff at the Cambridge Computational Biology Institute. I am currently a PI in the Cambridge Systems Biology Centre where I lead the Computational Proteomics Unit.

Posts by Laurent Gatto

<prev • 191 results • page 2 of 20 • 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 4 months ago by Laurent Gatto880
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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 months ago by Laurent Gatto880
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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 5 months ago by Laurent Gatto880
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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 5 months ago by Laurent Gatto880
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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 5 months ago by Laurent Gatto880
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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 5 months ago by Laurent Gatto880
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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 6 months ago by Laurent Gatto880
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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 6 months ago by Laurent Gatto880
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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 6 months ago by Laurent Gatto880
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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 6 months ago by Laurent Gatto880

Latest awards to Laurent Gatto

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
Popular Question 7 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 21 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 21 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 2.3 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.3 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 2.3 years ago, created 100 posts.
Supporter 3.3 years ago, voted at least 25 times.
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.

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