R help - Sep 2003 - 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

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