[BioC] Difficulty in AnnotatedDataFrame

[James F. Reid]

Hi Deepak,

you need to construct an AnnotatedDataFrame in the following way:
AnnotatedDataFrame(data=df, varMetaData=metaData)
Look-up the help page which is well documented:
help("AnnotatedDataFrame")

HTH.
J.

On 02/03/12 10:11, Deepak Datta wrote:
> 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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