Daphne Autran
2003-Sep-11 19:48 UTC
[R] Using R for microarrays datas analysis by Mixed model ANOVA. lme function.
Hi, We are using R to analyse microarrays datas by ANOVA. We would like to set up Mixed Model analysis, using the "lme" function within the nmle package. However, we have problem in understanding and getting the right formula to build a "groupedData" object which appear to be required for lme to work. I ve read all the available nmle package s Users guides and manuals, but explications are scarce. Does anybody have an experience in using this function for microarrays datas analysis and could send me informations or, if possible, a resolved exemple (input table of datas, formula of the model, ouput...) ? Maybe other R functions are usefull and easier to implement Mixed Models ANOVA for microarrays analysis, any suggestions ? I thank you in advance for your reply. Sincerely Daphne Autran Dr Daphne Autran Laboratory of Reproductive Development and Apomixis Department of Genetic Ingeniering CINVESTAV - Unidad Irapuato Km 9,6 Libramiento Norte A.P.629 C.P. 36500 Irapuato Guanajuato MEXICO Tel : (0052) 462 623 9600 ext.404 Fax : (0052) 462 624 5849 Email : dautran at ira.cinvestav.mx
Spencer Graves
2003-Sep-11 20:05 UTC
[R] Using R for microarrays datas analysis by Mixed model ANOVA. lme function.
1. Have you consulted Pinhiero and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? This is the standard (almost indispensible) reference on "lme". 2. Are you familiar with the Bioconductor project (www.bioconductor.org)? The have a substantial library of software for analyzing microarray data. hope this helps. spencer graves Daphne Autran wrote:> Hi, > We are using R to analyse microarrays datas by ANOVA. > We would like to set up Mixed Model analysis, using the "lme" function > within the nmle package. > However, we have problem in understanding and getting the right formula to > build a "groupedData" object which appear to be required for lme to work. > I ve read all the available nmle package s Users guides and manuals, but > explications are scarce. > > Does anybody have an experience in using this function for microarrays datas > analysis and could send me informations or, if possible, a resolved exemple > (input table of datas, formula of the model, ouput...) ? > > Maybe other R functions are usefull and easier to implement Mixed Models > ANOVA for microarrays analysis, any suggestions ? > > I thank you in advance for your reply. > Sincerely > > Daphne Autran > > > > > Dr Daphne Autran > > Laboratory of Reproductive Development and Apomixis > Department of Genetic Ingeniering > CINVESTAV - Unidad Irapuato > Km 9,6 Libramiento Norte > A.P.629 > C.P. 36500 Irapuato Guanajuato > MEXICO > > Tel : (0052) 462 623 9600 ext.404 > Fax : (0052) 462 624 5849 > Email : dautran at ira.cinvestav.mx > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help