hii... this is Deepak....

i am working on analysis of microarray data.

We tried using this code snippet
phenoData(spikein95) <- new("phenoData", pData = pd, varLabels = vl)

but it said that phenoData is now defunct and we need to use
AnnotatedDataFrame. And i am not able to proceed because of the following
error

AnnotatedDataFrame(x1)<-new("AnnotatedDataFrame",pData=pd, varLabels=v1)
Error in .nextMethod(.Object, ...) :
  invalid names for slots of class “AnnotatedDataFrame”: pData, varLabels


i am basically trying to segregate the samples into 3 parts containing
normal, HSIL and SCC data and this is the code that i have used till now...

setwd("E:\\Project\\CEL files\\Old\\GSE7803-3")
> f1=list.celfiles(path="E:\\Project\\CEL files\\Old\\GSE7803-3")
> x1<-ReadAffy(filenames=f1)
>  pd <- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2, 2,
+  2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3),
+  replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,4,5,6,7,
+  1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21))
> rownames(pd) <- sampleNames(x1)
> v1 <- list(population = "1 is normal, 2 is HSIL, 3 is SCC",
replicate="arbitary numbering")


i further wish to perform rma and then generate a MA plot.

kindly help me rectify this error and if possible explain with an example
so that i could proceed further.

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