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.
data(vac18.simulated)A list containing the following components:
genesdata frame with 48 rows and 500 columns. The simulated expression of 500 genes for 48 subjects.
samplea vector indicating the repeated measurements on each unique subject. See Details.
stimulationa factor indicating the stimulation condition on each sample.
timea factor indicating the time condition on each sample.
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).
Liquet, B., Le 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.