Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto1.0k
Reputation:
1,040
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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 week, 4 days ago
Joined:
11 years, 5 months ago
Email:
l************@gmail.com

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 • 228 results • page 1 of 23 • next >
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Answer: A: What does component or SCX classification in iTRAQ/TMT experiment represent?
... SCX is strong cation exchange. I assume component here means 10 fractions that were then analysed my LC-MSMS. ...
written 11 days ago by Laurent Gatto1.0k
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Comment: C: What does component or SCX classification in iTRAQ/TMT experiment represent?
... Could you provide some details? Where have you read this, in what context?   ...
written 11 days ago by Laurent Gatto1.0k
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Answer: A: mzR Error (different Version)
... It's not an error, it's only a warning and you can safely ignore it. It tells you that mzR was built with a different Rcpp version than is installed on your system. This used to be a problem, but now that Rcpp is stable, it's become irrelevant. ...
written 27 days ago by Laurent Gatto1.0k
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Answer: A: msmsTests, NA values in test.results output
... I'll attempt an answer here. I would suggest you reformulate your logical operator that checks whether you have any missing or negative values. The double operators && and || can be very confusing. Here's an example showing that they don't necessarily work in cases such as yours. > x ...
written 7 weeks ago by Laurent Gatto1.0k
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Comment: C: msmsTests, NA values in test.results output
... I didn't mean to attach it, but run all the commands in your R session, then copy the whole lot and their output and paste it here. For example: > library(msdata) > library(MSnbase) > f <- msdata::proteomics(full.names = TRUE, pattern = "TMT11") > f [1] "/home/lgatto/R/x86_64-pc-li ...
written 7 weeks ago by Laurent Gatto1.0k
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Comment: C: msmsTests, NA values in test.results output
... It's difficult to say much without the actual code and it's output, as it is executed in R. Two things though there are warnings at the end of your sessionInfo; I would recommend fixing them befoe doing anything else. Re-installing the packages light help. If you have issues or more questions about ...
written 7 weeks ago by Laurent Gatto1.0k
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Job: Research software engineer at the de Duve Institute, UCLouvain (Brussels, Belgium)
... The Computational Biology (CBIO) unit at the de Duve Institute in Brussels, Belgium, seeks to appoint a full time research software engineer. The successful candidate will join the research group of Professor Laurent Gatto and will have the opportunity to work on projects across a broad range of bio ...
job bioconductor teaching software engineer written 7 weeks ago by Laurent Gatto1.0k
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Comment: C: msmsTests, NA values in test.results output
... It would probably be helpful to provide code, detailed output and possibly example data. Also, don't forget to add the output of `sessionInfo()`. ...
written 7 weeks ago by Laurent Gatto1.0k
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Comment: C: msmsTests, NA values in test.results output
... Do you have any `NA` values in your original count data by any chance? ...
written 7 weeks ago by Laurent Gatto1.0k
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Answer: A: quantify() method for MSnExp to MSnSet for MS1 level data only
... In your question, you mention that the data was supposed to be MS/MS - does that mean to you were supposed to quantify in MS2, or only that the MS2 for identification is missing? Assuming it the latter, quantify() doesn't work (yet) for MS1 quantitation. You could look at the rawDiag package or xcms ...
written 12 weeks ago by Laurent Gatto1.0k

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Scholar 5 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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