Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto920
Reputation:
920
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
10 years, 10 months ago
Email:
l************@gmail.com

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 • 212 results • page 1 of 22 • next >
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Answer: A: How to manipulate assayData in MSnSetList
... Yes, indeed, this doesn't work because there is no replacement method for the assayData of an item in an MSnSetList. This however seems to work exprs(dun@x[[1]])[1,1] <- 1 It is a bit ugly, but might sort you out for now. I'll see to add proper replacement methods. ...
written 13 days ago by Laurent Gatto920
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Comment: C: Cannot install and load MSstats package
... And what happens when you type utils::warnErrList? If you get something like Error: 'warnErrList' is not an exported object from 'namespace:utils' could you try to reinstall utils with BiocInstaller::biocLite("utils") and try again to load MSstats. ...
written 16 days ago by Laurent Gatto920
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Answer: A: Cannot install and load MSstats package
... 1. It would be more useful if you could run library("MSstats") without limiting any messages. 2. What is your sessionInfo(). 3. Could you confirm that you installed the package with BiocInstaller::biocLite("MSstats"). It might also help running BiocInstaller::biocLite() to make sure all packages a ...
written 16 days ago by Laurent Gatto920
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Answer: A: Error in parameter setting using svmOptimisation for pRoloc analysis
... In the end, the issues seemed to be related to installation issues, as, after reinstallation as well as me running the code on the data, the error couldn't be reproduced. ...
written 4 weeks ago by Laurent Gatto920
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Comment: C: Error in parameter setting using svmOptimisation for pRoloc analysis
... The markers still look a bit week (Golgi apparatus has 2 proteins, Peroxison has 4). The error comes from somewhere within the code, where table expects two vectors of the same length, and somehow they don't with your data: > table(letters[1:10], letters[1:9]) Error in base::table(...) : all a ...
written 5 weeks ago by Laurent Gatto920
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Comment: C: Error in parameter setting using svmOptimisation for pRoloc analysis
... Thank you. My first suggestion would be to increase the number of markers, especially for the Golgi, chromatin and peroxisome. As I said, ideally, try to get 13+ for each class. I can't say it this is the reason for the error you see (although I suspect it is), but even if it's not, currently, you ...
written 5 weeks ago by Laurent Gatto920
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Answer: A: Error in parameter setting using svmOptimisation for pRoloc analysis
... It is a bit difficult to provide an explanation at this stage. How many markers do you have for your sub-cellular classes? Could you paste the output of getMarkers - here's the output for the stem cell data: > library("pRoloc") > library("pRolocdata") > data(hyperLOPIT2015) > getMarker ...
written 5 weeks ago by Laurent Gatto920
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Comment: C: Adding annotation to MSnSet
... Thank you for the code snippet. This looks reasonable to me. If I follow, you would like to add additional metadata from UniProt. If so, you'll need to have a column in that data. that matches the database accession numbers you used to combine the features. You can use dplyr::left_join to join the f ...
written 6 weeks ago by Laurent Gatto920
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Answer: A: Adding annotation to MSnSet
... It would be useful to have some additional details on what you have done. I assume you have raw data that you read into R using readMSData. I also suspect you have identification data resulting from running MSGF+ (in this case through the Bioconductor package MSGFplus). Have you run addIdentificatio ...
written 6 weeks ago by Laurent Gatto920
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Comment: C: mzR installation on Ubuntu 16.04
... It could be related to the gcc version - I vaguely remember issues with more recent versions of ubuntu and gcc, but I don't think it was related to pthread/thread.o. What version of gcc do you have? ...
written 7 weeks ago by Laurent Gatto920

Latest awards to Laurent Gatto

Scholar 10 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 10 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 10 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 2.0 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 2.0 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: how can i import a Mass spectrometry data in R
Scholar 2.5 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.5 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 2.5 years ago, created 100 posts.
Supporter 3.5 years ago, voted at least 25 times.
Autobiographer 3.6 years ago, has more than 80 characters in the information field of the user's profile.

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