## User: etienne.thevenot

etienne.thevenot •

**20**- Reputation:
**20**- Status:
- New User
- Location:
- France
- Website:
- http://etiennethevenot...
- Last seen:
- 1 year, 2 months ago
- Joined:
- 4 years, 1 month ago
- Email:
- e***************@cea.fr

I have a background of mathematics (Master) and molecular and cellular neurobiology (PhD). I have been working in the field of computational metabolomics since 2010 at CEA (French government-funded technological research organisation) within the MetaboHUB infrastructure. My research focuses on statistical approaches for biomarker discovery (Thevenot et al, 2015). To enable multivariate modeling and feature selection with OPLS, I wrote the ropls bioconductor package. I have integrated several tools for normalization and quality control of LC-HRMS data, as well as univariate and multivariate statistical analysis, into the Workflow4Metabolomics infrastructure for computational metabolomics.

#### Posts by etienne.thevenot

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... Thanks for reporting this bug which has been fixed in the 1.13.2 version of ropls (dev).
Etienne.
...

written 14 months ago by
etienne.thevenot •

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... You cannot use symbols (but special characters work). A better option would be to use colors according to your classes (use a factor in the parColFcVn argument):
> library(ropls)
> data(sacurine)
> pcaModel <- opls(sacurine[["dataMatrix"]])
> plot(pcaModel, typeVc = "x-score", parLab ...

written 15 months ago by
etienne.thevenot •

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... Hi,
Below is an example of labels ("s1", "s2", ..., "sN"), where N is the total number of samples. You can use any character vector of length N. Does it answer your question?
Etienne.
> library(ropls)
> data(sacurine)
> pcaModel <- opls(sacurine[["dataMatrix"]])
> plot(pcaModel, p ...

written 15 months ago by
etienne.thevenot •

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Answer:
A: Error in ROPLS with LPS-DA

... Hi Abigail,
I ran the script below on your data (PCA and PLS-DA) without any error.
The modeling with PLS-DA does not appear significant (pQ2 = 0.1). In addition, since you have 1e3 times more variables than samples, the risk of overfitting is very high.
Best wishes,
Etienne.
sunDF <- read.t ...

written 17 months ago by
etienne.thevenot •

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Answer:
A: Error in ROPLS with LPS-DA

... Hi Abigail,
Did you check that there is any variable with constant value for all samples in your dataset?
Otherwise, could you share your "sunoesy" data with me (etienne.thevenot@cea.fr)?
Best wishes,
Etienne.
...

written 17 months ago by
etienne.thevenot •

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... Hi Mike,
In your dataset, the algorithm finds that the optimal number of component is 1. Hence, a score plot in two-dimensions is not returned.
By setting the number of predictive components to 2 (with 'predI = 2'), you will force the algorithm to compute the second component and thus the score-pl ...

written 23 months ago by
etienne.thevenot •

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... Dear Dominik,
By default, ropls automatically selects the optimal number of predictive (PLS) or orthogonal (OPLS) components. To do this, the algorithm checks if the addition of an additional component improves the predictions. Here the message indicates that even the first predictive component was ...

written 3.1 years ago by
etienne.thevenot •

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