Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto840
Reputation:
840
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Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 5 days ago
Joined:
10 years, 5 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 • 185 results • page 1 of 19 • next >
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Comment: C: Adding Identification Data to MSnbase MSn Experiment
... Could you provide your sessionInfo() output, please. It would probably also easier to help with the raw and corresponding mzid files? ...
written 6 weeks ago by Laurent Gatto840
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Answer: A: Extract whether list element is MS1 or MS2 from mzR::peaks() output
... I would suggest you give the MSnbase package a go and load your data as an MSnExp object: x <- readMSData("raw.mzML", mode = "onDisk") If you want only MS1 data, you can either filter your data x1 <- filterMsLevel(x, 1) or directly load MS1 data only x1 <- readMSData("raw.mzML", msLevel = 1 ...
written 7 weeks ago by Laurent Gatto840
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Answer: A: installing xcms and faahKO package
... I have seen similar issues in the past, where different libraries are available to different R installation run either directly or through RStudio on Windows and OSX. The way I have fixed it was to uninstall old R versions (that weren't used anyway), remove old libraries, possibly use that opportuni ...
written 7 weeks ago by Laurent Gatto840
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Answer: A: Combining two MSnSet
... Yes, it is possible using the combine method. This is described in Combining MSnSet instances section of the MSnbase: MS data processing, visualisation and quantification vignette. You can access it from R by typing vignette("MSnbase-demo", package = "MSnbase"). You can access it online here. Note ...
written 8 weeks ago by Laurent Gatto840
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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 12 weeks ago by Laurent Gatto840
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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 3 months ago by Laurent Gatto840
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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 3 months ago by Laurent Gatto840
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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 3 months ago by Laurent Gatto840
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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 3 months ago by Laurent Gatto840
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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 3 months ago by Laurent Gatto840

Latest awards to Laurent Gatto

Scholar 5 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 5 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 6 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 19 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 19 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 21 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.1 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.1 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 2.1 years ago, created 100 posts.
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