At 06:18 AM 25/06/2003, leon ding wrote:
>Hi,
>
>I tried to use limma two-sample experiment. I got error when doing
lm.series.
>
>below is the scripts of what happened. Could somebody tell me what is
>going wrong?
>
>Leon
>
> > RG <- read.maimages(slides,source="genepix",wt.fun=wtflags(0.0))
>Read s1.gpr
>Read s2.gpr
>Read s3.gpr
>Read c1.gpr
>Read c2.gpr
>Read c3.gpr
> > RG$R[1:4,]
> s1 s2 s3 c1 c2 c3
>[1,] 640 1154 532 262 963 413
>[2,] 760 1085 511 220 507 286
>[3,] 2966 4866 1997 866 2186 978
>[4,] 588 871 396 286 678 304
> > MAraw <- MA.RG(RG)
> > MA <- normalizeWithinArrays(RG,layout)
> > design <- read.table("design.txt",header=TRUE,sep="\t",as.is=TRUE)
> > design
> ConRef SampCon
>s1 1 1
>s2 1 1
>s3 1 1
>c1 1 0
>c2 1 0
>c3 1 0
> > fit <- lm.series(MA$M,design)
>Error in as.double.default(structure(list(ConRef = c(1, 1, 1, 1, 1,
1), :
> (list) object cannot be coerced to vector type 14
Well, this is one of those somewhat subtle things in R which LIMMA is
not
yet developed enough to protect you from. The function 'read.table'
creates
a 'data.frame', which is like a spreadsheet in excel. A 'data.frame'
can
sometimes be treated as a 'matrix', but it is not a matrix. On the
other
hand, 'lm.series' expects to get a matrix for the design matrix. So
you need
design <- as.matrix(design)
fit <- lm.series(MA$M, design)
Gordon
