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, 3 days 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 2 of 22 • next >
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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 11 weeks ago by Laurent Gatto920
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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 11 weeks ago by Laurent Gatto920
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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 11 weeks ago by Laurent Gatto920
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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 11 weeks ago by Laurent Gatto920
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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 11 weeks ago by Laurent Gatto920
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Comment: C: calling combineFeatures twice causes duplicate row.names
... It should be `cv = FALSE` in lower case - sorry for the confusion. ...
written 11 weeks ago by Laurent Gatto920
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Comment: C: calling combineFeatures twice causes duplicate row.names
... Thank you for your answer - I'll investigate the CV = FALSE issue. ...
written 11 weeks ago by Laurent Gatto920
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Answer: A: calling combineFeatures twice causes duplicate row.names
... Thank you for the report. The error happens because every time combineFeatures is called, is estimates the coefficient of variations for each column and adds these to the feature data. Here, these feature variable already exists when summarising the data from peptide to proteins. I have opened an i ...
written 12 weeks ago by Laurent Gatto920
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Comment: C: Combining two MSnSet
... Thank you for the report - fixed on github and (soon) in devel. ...
written 12 weeks ago by Laurent Gatto920
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Comment: C: Combining two MSnSet
... It's not clear what you are reporting here, an error or a warning? The warnings you see there could be related to different levels in the feature variables. Could you try to set the Experiment variable to a character to check. It is difficult to say more with additional details about the MSnSets. C ...
written 12 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 11 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 2.2 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
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