Moderator: Laurent Gatto

gravatar for Laurent Gatto
Laurent Gatto810
Reputation:
810
Status:
Trusted
Location:
United Kingdom
Website:
http://lgatto.github.io/
Twitter:
lgatt0
Scholar ID:
Google Scholar Page
Last seen:
8 hours ago
Joined:
9 years, 12 months 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 • 169 results • page 1 of 17 • next >
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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 6 days ago by Laurent Gatto810
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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 6 days ago by Laurent Gatto810
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Job: Post-doctoral mass spectrometry and proteomics bioinformatician
... 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 9 days ago by Laurent Gatto810
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Comment: C: Limma is doing the right way to calculate the fold change?
... Yes: the intensity increases upon treatment. ...
written 10 days ago by Laurent Gatto810
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Comment: C: Limma is doing the right way to calculate the fold change?
... See @SamGG 's comment. Also, the log2 fold-changes are symetrical, so -1759.8 when comparing control vs. treatment becomes 1759.8 when comparing treatment vs control. ...
written 10 days ago by Laurent Gatto810
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Answer: A: Limma is doing the right way to calculate the fold change?
... From the data you show at the top, all proteins are down-regulated because the intensities in your controls are lower than in your treatment, hence negative log2 fold-changes. If it is the negative values that confuse you, it is because down-regulation (i.e fold-changes between 0 and 1) become nega ...
written 10 days ago by Laurent Gatto810
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Answer: A: Application of Deseq2 to mass spec data
... The only type of MS-based quantitation that is amenable to DESeq2 (or similar approaches) is spectral counting. Other approaches, whether labelled of unlabelled, are continuous data; I would also recommend limma for their analysis. ...
written 18 days ago by Laurent Gatto810
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Answer: A: mzR (2.8.1) Rcpp (0.12.10) compiler linker issue in Bioconductor 3.4, R 3.3.3
... I don't think the error you see is a linker issue. The problem is that the files that you want to read are cdf files [12] "/home/lg390/R/x86_64-pc-linux-gnu-library/3.4/faahKO/cdf/WT/wt22.CDF" > basename(cdf_files) [1] "ko15.CDF" "ko16.CDF" "ko18.CDF" "ko19.CDF" "ko21.CDF" "ko22.CDF" [7] "wt1 ...
written 10 weeks ago by Laurent Gatto810
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Answer: A: mzR failure installation
... I am following up about this issue which has been resolved. Details available here.   ...
written 3 months ago by Laurent Gatto810

Latest awards to Laurent Gatto

Scholar 9 days ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 10 days ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Popular Question 27 days ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 14 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 14 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 16 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 20 months ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 20 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Centurion 20 months ago, created 100 posts.
Supporter 2.7 years ago, voted at least 25 times.
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