Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto840
Reputation:
840
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 2 days ago
Joined:
10 years, 4 months ago
Email:
l****@cam.ac.uk

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 • 185 results • page 2 of 19 • 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 4 months ago by Laurent Gatto840
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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 4 months ago by Laurent Gatto840
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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 4 months ago by Laurent Gatto840
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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 4 months ago by Laurent Gatto840
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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 4 months ago by Laurent Gatto840
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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 4 months ago by Laurent Gatto840
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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 months ago by Laurent Gatto840
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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 months ago by Laurent Gatto840
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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 ...
proteomics job bioinformatics mass spectrometry written 5 months ago by Laurent Gatto840
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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 months ago by Laurent Gatto840

Latest awards to Laurent Gatto

Scholar 5 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 5 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 5 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 19 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 19 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 2.1 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.1 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 2.1 years ago, created 100 posts.
Supporter 3.1 years ago, voted at least 25 times.
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