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Moderator: Laurent Gatto

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Laurent Gatto1.1k
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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 • 237 results • page 1 of 24 • next >
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Comment: C: Protein quantification by MSnbase package
... Yes, you could do quantitation in `MSnbase`, depending on your MS quantitation methodology employed. However, from you mail above, it doesn't seem that you have the raw data anyway. Also, it is unclear what quantitation methodology was used - it could be spectral counting, or may be the quantitation ...
written 1 day ago by Laurent Gatto1.1k
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Answer: A: How to convert a xlsx data file to MSnSet format?
... - First of all, you can set `sep = ","` when exporting and `MSnSet` to a spreadsheet. Alternatively, you could also read the data in with `readMSnSet2` and set `sep = "\t"`. - In `write.exprs`, you can define to also export the feature variables - you can provide feature variables one by one, of a ...
written 7 days ago by Laurent Gatto1.1k
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Answer: A: How to convert a xlsx data file to MSnSet format?
... You have two options. 1. Open your xlsx file with Excel and export it to csv, the use `readMSnSet2` to load it into R as an `MSnSet` 2. Import your xlsx file into R as a `data.frame` and use that `data.frame` as input to `readMSnSet2` to create an `MSnSet` Have a look at `?readMSnSet2` or in the v ...
written 10 days ago by Laurent Gatto1.1k
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Comment: C: MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repositor
... This could be something on your side. Are you behind a firewall? Could you try to set `setInternet2(TRUE)` or see these other related issues: https://stackoverflow.com/questions/33355444/r-when-trying-to-install-package-internetopenurl-failed and https://stackoverflow.com/questions/25599943/unable-t ...
written 4 weeks ago by Laurent Gatto1.1k
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Answer: A: MSnbase package, Error in downloading data file "PXD000001" from PRIDE Repositor
... It looks like there was a problem to access and download files from the PRIDE ftp server. Things seem to work on my end now: > library(rpx) > px1 <- PXDataset("PXD000001") > px1 Object of class "PXDataset" Id: PXD000001 with 12 files [1] 'F063721.dat' ... [12] ...
written 4 weeks ago by Laurent Gatto1.1k
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Comment: C: MSnset combine error message
... Ok, let me know how it goes. The feature variables (in `fData`) can also lead to errors if they have the same names in different objects. For example if the number of peptides for a protein group in the first object claims that 10 peptides were found, but in the second object only 8 peptides were fo ...
written 5 weeks ago by Laurent Gatto1.1k
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Comment: C: Errors installing RforProteomics and MSnbase packages
... In addition to @SamGG's answer, you could also try to set up a different CRAN mirror. Using `0-Cloud [https]` (the first option) with `chooseCRANmirror()` allows me to run `BiocManager::install("colorspace")` successfully. ...
written 5 weeks ago by Laurent Gatto1.1k
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Answer: A: MSnset combine error message
... From the dimensions of your 4 objects, I assume that the 10 sample (column) names are identical and that you want to combine along to features (rows). Could it be that `MSnset_Set4` has a feature that exists in a previous object? This would indeed lead to such an error. ...
written 5 weeks ago by Laurent Gatto1.1k
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Answer: A: MSnbase annotate m/z values on mass spectrum plots
... You can add a sequence (as a character) to plot to automatically annotate the plot. Below I have sp, an object of class Spectrum, and its sequence s: > sp Object of class "Spectrum2" Precursor: 641.3205 Retention time: 30:2 Charge: 2 MSn level: 2 Peaks count: 121 Total ion count: 58841 ...
written 10 weeks ago by Laurent Gatto1.1k
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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 12 weeks ago by Laurent Gatto1.1k

Latest awards to Laurent Gatto

Scholar 8 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Does OnDiskMSnExp rewrite original data
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Selecting genes based on expressional variance
Scholar 9 months ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 9 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
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Scholar 20 months ago, created an answer that has been accepted. For A: Limma is doing the right way to calculate the fold change?
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: how can i import a Mass spectrometry data in R
Popular Question 21 months ago, created a question with more than 1,000 views. For Installation of TxDb.Hsapiens.UCSC.hg19.knownGene fails.
Scholar 2.9 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 2.9 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
Scholar 3.0 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
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Scholar 3.4 years ago, created an answer that has been accepted. For A: how can i import a Mass spectrometry data in R
Scholar 3.4 years ago, created an answer that has been accepted. For A: Converting Synapter object output into a MSnbase-compatible object
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Autobiographer 4.4 years ago, has more than 80 characters in the information field of the user's profile.

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