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 ---------------------------------------- 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 SOSTIENI LA RICERCA: devolvi il 5 per mille delle imposte alla FONDAZIONE INGM Istituto Nazionale Genetica Molecolare di Milano. Devi solo inserire il codice fiscale della Fondazione - 04175700964 - in tutti i modelli CUD, 730 e UNICO nella sezione relativa al finanziamento per la ricerca scientifica. [[alternative HTML version deleted]]

You could start by looking at limma and maanova. In limma, you would treat patients as blocks. Limma allows only one random effect. I have not used maanova, but I believe it allows multiple random effects. --Naomi At 05:56 AM 8/10/2009, Riccardo Rossi wrote: >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 > > > >---------------------------------------- >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 at ingm.it >www.ingm.it >SOSTIENI LA RICERCA: devolvi il 5 per mille delle imposte alla >FONDAZIONE INGM Istituto Nazionale Genetica Molecolare di Milano. >Devi solo inserire il codice fiscale della Fondazione - 04175700964 >- in tutti i modelli CUD, 730 e UNICO nella sezione relativa al >finanziamento per la ricerca scientifica. > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111