After preprocessing .cel files through RMA  log 2 transformation (code is given below) i want to do linear models limma so for that i follow linear model limma tutorial (the code is given below) there is an error kindly if some one know about linear models"limma" so guide me. I read in another tutorial about target files but i dont understand the criteria of selecting target files .

RMA

library(affy)
library(hgu133a.db)
library(hgu133acdf)

raw.data = ReadAffy(verbose = FALSE, filenames = cels, cdfname = "hgu133acdf")

data.rma.norm = rma(raw.data)

rma = exprs(data.rma.norm)

write.table(rma, file = "rma.txt", quote = FALSE, sep = "\t")

limma

>  data <- ReadAffy()
>  eset <- rma(data)

Background correcting
Normalizing
Calculating Expression
Warning messages:
1: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133acdf’
2: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133acdf’
>  design <- model.matrix(~ 0+factor(c(1,1,1,2,2,3,3,3)))
> colnames(design) <- c("group1", "group2", "group3")
> library(limma)

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

    plotMA

>  fit <- lmFit(eset, design)
Error in lmFit(eset, design) :
  row dimension of design doesn't match column dimension of data object

Well, the problem is that you have 9 arrays but you have created the design matrix as if there are 8 arrays -- the error is telling you to check your design matrix.

I am guessing that you meant to write:

design <- model.matrix(~ 0+factor(c(1,1,1,2,2,2,3,3,3)))

i.e., you meant to have 3 arrays in each group instead of just 2 in group 2.