Moderator: Laurent Gatto

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Laurent Gatto1.0k
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http://lgatto.github.io/
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lgatt0
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I am a Professor of Bioinformatics at the de Duve Institute, at the UCLouvain, Belgium. 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. Since 2010, I have been focusing 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.

Posts by Laurent Gatto

<prev • 225 results • page 2 of 23 • next >
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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 4 months ago by Laurent Gatto1.0k
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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 5 months ago by Laurent Gatto1.0k
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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 5 months ago by Laurent Gatto1.0k
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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 6 months ago by Laurent Gatto1.0k
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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 6 months ago by Laurent Gatto1.0k
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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 6 months ago by Laurent Gatto1.0k
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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 7 months ago by Laurent Gatto1.0k
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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 7 months ago by Laurent Gatto1.0k
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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 7 months ago by Laurent Gatto1.0k
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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 7 months ago by Laurent Gatto1.0k

Latest awards to Laurent Gatto

Scholar 4 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Does OnDiskMSnExp rewrite original data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Selecting genes based on expressional variance
Scholar 5 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
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Scholar 16 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
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