Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto820
Reputation:
820
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
2 days, 1 hour ago
Joined:
10 years, 1 month ago
Email:
l****@cam.ac.uk

Laurent Gatto is a senior research associate in the Department of Biochemistry, University of Cambridge and a visiting scientist in the PRIDE team at the EBI. He graduated in Biology from the Free University of Brussels, Belgium, and subsequently earned his PhD in Evolutionary Biology. He pursued his education at the University of Namur studying Computer Science before working in industry on genetic and transcriptomic data analysis. In January 2010, he joined the Cambridge Centre for Proteomics to work on quantitative and organelle proteomics and. In August 2013, he established the Computational Proteomics Unit in the Cambridge System Biology Centre.

Posts by Laurent Gatto

<prev • 175 results • page 1 of 18 • next >
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Comment: C: Post-doctoral mass spectrometry and proteomics bioinformatician (updated)
... This position hasn't been filled and is being re-advertised. ...
written 2 days ago by Laurent Gatto820
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Comment: C: qcmetrics package and longitudinal qc data
... Hi Eralp, The function above looks sensible. I would suggest you use readMSData2 as it will be much faster (it won't read the raw data into memory), but you'll need to make sure you also define the MS level that you wish to read (by default, it reads all levels). Also, you can probably drop the c() ...
written 2 days ago by Laurent Gatto820
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Answer: A: Problem in installing bioconductor
... The message you show looks good - this is exactly what you are supposed to see. Now, you need to decide what package to use depending on the type of data you have and analysis you want to do.     ...
written 13 days ago by Laurent Gatto820
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Answer: A: qcmetrics package and longitudinal qc data
... Your question is not clear to me. Could you clarify what you are trying to do and/or answer the following questions. Are you replicating the example for raw MS data shown in the qcmetrics vignette, or are you creating you own QcMetric objects? What is your input format, and what operability with ...
written 13 days ago by Laurent Gatto820
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Comment: C: Problem with mzR and/or Rcpp?
... Note also that you are using a somewhat old version of R (current version is 3.4.1) and, as a result, the old release of Bioconductor. You won't be able to get the latest mzR (that is using the latest Rcpp) without a more recent R. ...
written 19 days ago by Laurent Gatto820
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Answer: A: Problem with mzR and/or Rcpp?
... What you see is a warning that highlights the version mismatch. In most cases, it can be ignored and everything will work as expected. In the past, when Rcpp had more substantial changes, error happened. If this happens, please report back. Otherwise, enjoy mzR and msPurity. ...
written 19 days ago by Laurent Gatto820
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Answer: A: P-value distribution acceptable for qvalue
... The distribution certainly look weird, and it would be important to understand why they show such a conservative trend. Could it be that their have already been adjusted? This post is relevant. Anyway, applying qvalue, or any adjustment, is not going to be of any help without first troubleshooting ...
written 5 weeks ago by Laurent Gatto820
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Answer: A: DESeq2: Error: could not find function "vst"
... You need to update your version of R (current version is 3.4, you are still using 3.2), which will get you the latest version of DESeq2 (v 1.16.0, you have 1.10.1) and vst, which was introduced in version 1.12.0. ...
written 5 weeks ago by Laurent Gatto820
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Job: Post-doctoral mass spectrometry and proteomics bioinformatician (updated)
... The Cambridge Centre for Proteomics (CCP) is currently looking to recruit an experienced post-doctoral bioinformatician within its core facility unit. The successful candidate will be required to analyse high-throughput proteomics datasets using numerous proteomic software packages (e.g. Proteome D ...
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Answer: A: The data is not in the file that it should be
... The hyperLOPIT2015 data lives in the pRolocdata package, which you need to load first: > library("pRolocdata") > data(hyperLOPIT2015) > hyperLOPIT2015 MSnSet (storageMode: lockedEnvironment) assayData: 5032 features, 20 samples element names: exprs protocolData: none phenoData sampleN ...
written 5 weeks ago by Laurent Gatto820

Latest awards to Laurent Gatto

Scholar 5 weeks ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 5 weeks ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 15 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 15 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 17 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 21 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 21 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 21 months ago, created 100 posts.
Supporter 2.8 years ago, voted at least 25 times.
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