Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto980
Reputation:
980
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
2 months ago
Joined:
11 years, 1 month 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 • 217 results • page 1 of 22 • next >
0
votes
1
answers
97
views
1
answers
Comment: C: mZR: access "parentFile" tag
... Yes, it's exactly something like that I was thinking of. Note that there's the fileNames function to extract the file name of the mz[X]ML file, but that can be different than the original file. > library("MSnbase") > ms <- readMSData("file.mzML", mode = "onDisk") > (f <- fileNames(m ...
written 8 weeks ago by Laurent Gatto980
0
votes
1
answers
97
views
1
answers
Comment: C: mZR: access "parentFile" tag
... I was rather thinking about accessing the relevant information by extracting it from the XML file directly (using the `XML` or `xml2` packages), rather than converting it to a database. The latter is an interesting approach which has advantages, but is a bit too heavy-handed to extract a single tag. ...
written 9 weeks ago by Laurent Gatto980
0
votes
1
answers
97
views
1
answers
Answer: A: mZR: access "parentFile" tag
... No, I don't think so. In addition, it looks like that tag is different in mzML files, which we tend to develop for now. This is something that we could consider adding and shouldn't be too difficult using xml2 - PR on github welcome.   ...
written 10 weeks ago by Laurent Gatto980
0
votes
1
answers
107
views
1
answers
Answer: A: Thermo Xcalibur RAW data to MGF
... The short answer is no, because to access (and this convert) proprietary Thermo raw data, you need to their libraries that are only available on Windows. That would mean that an R package would need to (i) incorporate these proprietary binary Thermo libraries and (ii) only be available on Windows. Y ...
written 12 weeks ago by Laurent Gatto980
0
votes
1
answers
88
views
1
answers
Answer: A: Label free quantification post FDR calculation for MS/MS Proteomics
... If you want to do spectral counting, you can proceed from an MSnID workflow to MSnbase by converting your MSnID objects to MSnSet data using the as method, as documented at the end of the MSnID vignette. You could then combine multiple MSnSet data object (for different samples) using the combine met ...
written 3 months ago by Laurent Gatto980
0
votes
2
answers
80
views
2
answers
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 4 months ago by Laurent Gatto980
0
votes
1
answers
168
views
1
answers
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 4 months ago by Laurent Gatto980
0
votes
1
answers
168
views
1
answers
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 4 months ago by Laurent Gatto980
0
votes
2
answers
146
views
2
answers
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 5 months ago by Laurent Gatto980
0
votes
2
answers
146
views
2
answers
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 months ago by Laurent Gatto980

Latest awards to Laurent Gatto

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Selecting genes based on expressional variance
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: Converting Synapter object output into a MSnbase-compatible object
Scholar 13 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Voter 13 months ago, voted more than 100 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Scholar 14 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: how can i import a Mass spectrometry data in R
Popular Question 14 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 2.3 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
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 2.5 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Centurion 2.8 years ago, created 100 posts.
Scholar 2.8 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.8 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Supporter 3.9 years ago, voted at least 25 times.
Autobiographer 3.9 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 312 users visited in the last hour