[BioC] lm.series error

[Ramon Diaz-Uriarte]

Dear Delphine,

How exactly did you create "design"? Try d1 <- as.matrix(design) and then 
using d1 in lm.series.

Ramón

On Thursday 21 August 2003 14:51, Delphine Fleury wrote:
> Dear all,
> I want to analyse my affy data with limma. I have 3 genotypes A, B, C I
> want to compare to the reference ref, and 3 replicates for each genotype
>
> and ref, so 12 arrays. I have this error message I don t understand:
> > data<-ReadAffy()
> > eset<-rma(data)
> >
> > design
>
>             ref A B C
> Exp143hyb246   1   0   0   0
> Exp143hyb247   1   1   0   0
> Exp143hyb248   1   0   1   0
> Exp143hyb249   1   0   0   1
> Exp143hyb410   1   0   0   0
> Exp143hyb411   1   0   0   0
> Exp143hyb412   1   1   0   0
> Exp143hyb413   1   1   0   0
> Exp143hyb414   1   0   1   0
> Exp143hyb415   1   0   1   0
> Exp143hyb416   1   0   0   1
> Exp143hyb417   1   0   0   1
>
> > fit<-lm.series(exprs(eset), design)
>
> Error in as.double.default(structure(list(ler = c(1, 1, 1, 1, 1, 1, 1,
>
>         (list) object cannot be coerced to vector type 14
>
> What's wrong with my design ?
> Thanks
>
> Delphine
>
>
>
>
> --
> ==================================================================
> Delphine Fleury
> DEPARTMENT OF PLANT SYSTEMS BIOLOGY           Fax:32 (0)9 3313809
> GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
> Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
> mailto:defle at psb.ugent.be                  http://www.psb.ugent.be
>
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-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://bioinfo.cnio.es/~rdiaz