Moderator: Laurent Gatto

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Laurent Gatto980
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980
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Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
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Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
11 years 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 2 of 22 • next >
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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 4 months ago by Laurent Gatto980
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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 4 months ago by Laurent Gatto980
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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 4 months ago by Laurent Gatto980
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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 4 months ago by Laurent Gatto980
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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 4 months ago by Laurent Gatto980
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Comment: C: Using Human Protein Atlas annotations with pRoloc to interpretate subcellular lo
... Re when you say "I want to use the Human Protein Atlas (HPA) instead because it has a finer scale of information for the subcellular location." This is of course a good approach, but whether this can be done also depends on the resolution in your data. If there aren't enough sub-nuclear markers o ...
written 5 months ago by Laurent Gatto980
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Comment: C: Trouble using addMarkers from pRoloc on my own dataset
... Re PCA plot, the funny share of the points is because you have integers. You should start by removing proteins that have only 0 rows (and possibly those that have few and low values), then try to rescale between 0 and 1 (use normalise(e, method = "sum")). But even with this pre-processing, I think ...
written 5 months ago by Laurent Gatto980
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Comment: C: Trouble using addMarkers from pRoloc on my own dataset
... You can use whatever you want as feature names. The default is to use indices, but you can also set then with readMSnSet2(..., fnames = "UNIPROT") - see ?readMSnSet2 for details about fnames. You can also set the feature names later with featureNames(e) <- fData(e)$UNIPROT ...
written 5 months ago by Laurent Gatto980
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Answer: A: Trouble using addMarkers from pRoloc on my own dataset
... You need to tell addMarkers how to match the proteins in the MSnSet and in the marker vector. > ## named marker vector > hsap <- pRolocmarkers("hsap") > head(hsap) P08865 P0CW22 P15880 P22090 P23396 "40S Ribosome" "40S Ribosome" "40S Ribosome" "4 ...
written 5 months ago by Laurent Gatto980
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Answer: A: Using Human Protein Atlas annotations with pRoloc to interpretate subcellular lo
... Markers are defined as proteins that localise to a sub-cellular niche with high confidence. They are subsequently used to infer localisation of non-markers proteins (of unknown localisation), hence the need for high confidence for all or most markers. They are often defined based on a set of organel ...
written 5 months ago by Laurent Gatto980

Latest awards to Laurent Gatto

Scholar 9 weeks ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 9 weeks ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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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 13 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 13 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 13 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
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Scholar 2.8 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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