[BioC] limma Two-sample model

[leon ding]

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


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