Hello,

Is there a specific packafe or function to perform model 3 (mixed effects) ANOVAs on expression data? Is anyone able to address me to the correct bioc package/function if any? (I was not able so far.)

Here's the details of what I have and what I need to do:
1) the data
57 genelists, one list for each sample I have
These 57 genelists belongs to 17 different sample type, let's say cell populations
The 57 samples come from 30 different experiments (or sorting/purifications)
Basically is like having 57 samples grouped in 17 cell types obtained from 30 different patients, where "cell types" is a fixed factor and "patients" is a random factor (infact samples belonging to each cell population come from different patients/sorting, according to availability of the moment)
2) what I need to do
I would like to pick genes significantly differentially expressed among the 17 samples, considering also the "contribute" of the random factor (patients, i.e. sorting) to sample variability. So far I only made 1way (model1) ANOVAs considering the cell populations grouping (fixed effect), I need to make a Model3 (mixed effect) ANOVA considering also the sorting/purification grouping as a random effect.

Thanks to everyone!,
Ric



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Riccardo L. Rossi, PhD
Integrative Biology Program
Fondazione INGM
Via F. Sforza 28
20122 Milano, IT
phone: +39 02 00662326
fax: +39 02 00662346
rossi@ingm.it
www.ingm.it
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