vac18.simulated: Simulated data based on the vac18 study for multilevel...

In mixOmics: Omics Data Integration Project

Description

Simulated data based on the vac18 study to illustrate the use of the multilevel analysis for one and two-factor analysis with sPLS-DA. This data set contains the expression simulated of 500 genes.

Usage

data(vac18.simulated)

Format

A list containing the following components:

list("genes")

data frame with 48 rows and 500 columns. The simulated expression of 500 genes for 48 subjects.

list("sample")

a vector indicating the repeated measurements on each unique subject. See Details.

list("stimulation")

a factor indicating the stimulation condition on each sample.

list("time")

a factor indicating the time condition on each sample.

Details

In this cross-over design, repeated measurements are performed 12 experiments units (or unique subjects) for each of the 4 stimulations.

The simulation study was based on a mixed effects model (see reference for details). Ten clusters of 100 genes were generated. Amongt those, 4 clusters of genes discriminate the 4 stimulations (denoted LIPO5, GAG+, GAG- and NS) as follows: \ -2 gene clusters discriminate (LIPO5, GAG+) versus (GAG-, NS) \ -2 gene clusters discriminate LIPO5 versus GAG+, while GAG+ and NS have the same effect \ -2 gene clusters discriminate GAG- versus NS, while LIPO5 and GAG+ have the same effect \ -the 4 remaining clusters represent noisy signal (no stimulation effect) \

Only a subset of those genes are presented here (to save memory space).

Value

none

References

Liquet, B., Lê Cao, K.-A., Hocini, H. and Thiebaut, R. (2012). A novel approach for biomarker selection and the integration of repeated measures experiments from two platforms. BMC Bioinformatics 13:325.

mixOmics documentation built on April 15, 2021, 6:01 p.m.