[BioC] Difficulty in AnnotatedDataFrame

[James F. Reid]

Hi Deepak,

please keep the thread on the list for other users.

On 02/03/12 10:28, Deepak Datta wrote:
> hey James, i have read the help page and i did not find it helpful. i
> would really appreciate if you could please explain me with an example
> giving details on creating a metaData


something like this should work:

new("AnnotatedDataFrame",
     data=pd,
     varMetadata=data.frame(labelDescription=unlist(v1)))

since your v1 is a list (it needen't be).

Best.
J.

>
>
> On Fri, Mar 2, 2012 at 3:49 PM, James F. Reid
> <james.reid at ifom-ieo-campus.it <mailto:james.reid at ifom-ieo-campus.it>>
> wrote:
>
>     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.
>
>                 [[alternative HTML version deleted]]
>
>
>
>
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