Commit 99a72769 authored by Samuel BERTRAND's avatar Samuel BERTRAND 🐉

Update README.md

parent 07af84b2
......@@ -78,7 +78,7 @@ Then two result tables a provided. One corresponding to the selected features ca
The variables represented in pink in the volcano plot are those listed in the “result$featuresSelection” table. The parameters used for features selection can be modified within the function arguments “lim.FC” and “lim.pVal”.
<h2>Multivariate data analysis using OPLS-DA</h2>
The data analysis strategy corresponds to the direct comparison of samples from pure metabolomes with the mixed metabolome separately by a multivariate method called OPLS-DA (Orthogonal projection of latent structure with discriminant analysis) in a way similar to univariate analysis. In the cases presented here, “Fungi1” is compared to “Fungi1VSFungi2” and “Fungi2” is compared to “Fungi1VSFungi2” separately. Then the two data analysis are merged based on both VIP (variable importance in the projection) values.
The data analysis strategy corresponds to the direct comparison of samples from pure metabolomes with the mixed metabolome separately by a multivariate method called OPLS-DA (Orthogonal projection of latent structure with discriminant analysis) in a way similar to univariate analysis. In the cases presented here, “Fungi1” is compared to “Fungi1VSFungi2” and “Fungi2” is compared to “Fungi1VSFungi2” separately. Then the two data analysis are merged based on both VIP (variable importance in the projection) values.<br /><br />
Multivariate data analysis is achieved as follow:
......@@ -101,28 +101,28 @@ Again two result tables a provided. One corresponding to the selected features c
<th>...</th>
</tr>
<tr>
<th>OPLS.DA.VIP1 (Fungi1 / Fungi1VSFungi2)</th>
<th>OPLS.DA.VIP1 (pure metabolome1 / mixed metabolome)</th>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td></tr>
<tr>
<th>OPLS.DA.VIP1 (Fungi2 / Fungi1VSFungi2)</th>
<th>OPLS.DA.VIP1 (pure metabolome2 / mixed metabolome)</th>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td></tr>
<tr>
<th>OPLS.DA.p1 (Fungi1 / Fungi1VSFungi2)</th>
<th>OPLS.DA.p1 (pure metabolome1 / mixed metabolome)</th>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td></tr>
<tr>
<th>OPLS.DA.p2 (Fungi2 / Fungi1VSFungi2)</th>
<th>OPLS.DA.p2 (pure metabolome2 / mixed metabolome)</th>
<td></td>
<td></td>
<td></td>
......@@ -135,4 +135,8 @@ Again two result tables a provided. One corresponding to the selected features c
<td></td>
<td></td>
<td></td></tr>
</table>
\ No newline at end of file
</table>
The provided data corresponds to the VIP of both models to assess statistical significance (for more information please read https://bioconductor.org/packages/release/bioc/html/ropls.html). In addition, the p parameters for each variables as provided by ropls package is also reported as it allows to knows the change corresponds to an increase or decrease. Thus the p1+p2 values is important to select features induced in both OPLS-DA models.
The variables represented in pink in the SUS plot are those listed in the “result$featuresSelection” table. The parameters used for features selection can be modified within the function argument “lim.VIP”.
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