[BioC] lm.series error

[Gordon Smyth]

Dear Delphine,

At 10:51 PM 21/08/2003, 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)

The 'design' argument to lm.series needs to be a numeric matrix. Your 
'design' is a data.frame, as can be seen by the fact that it contains both 
character and numeric elements. You need

design <- as.matrix(design[,-1])

and then proceed to 'lm.series'. (Note that as.matrix(design) will not work 
as it will give you a character matrix!)

If you install the development version of limma, then you could use

fit <- lmFit(eset, design)

i.e., lmFit will work directly on exprSet objects.

Regards
Gordon

>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