Thanks a lot all of your helpful suggestions.

Yeah, I have struggled with this things for couples of days, I should have
an alternative way to make the life easier as u said.

Zhe

On 5 August 2010 18:59, Kasper Daniel Hansen
<kasperdanielhansen@gmail.com>wrote:

> You are putting your data into an ExpressionSet.  However, rma takes
> and AffyBatch as input and outputs an ExpressionSet, so you are using
> the wrong class.
>
> Having said that, you can usually find CEL files on ArrayExpress,
> which will make your life much easier.
>
> Kasper
>
> On Thu, Aug 5, 2010 at 11:19 AM, Zhe Liu <zhliu.tju@gmail.com> wrote:
> > Thanks a lot for your soon reply.
> >
> > I think this processed data in arrayexpress is not background corrected
> and
> > normalized, though it should be as normalized in MIAME data format.
> Because
> > the CHP:singal amount vary greatly. For example as below, some of them
> are
> > less than 100 but some of them are over thousands.
> >
> > 51.2
> > 78
> > 64.6
> > 136.3
> > 191.2
> > 530.7
> > 589.4
> > 2594.6
> > 2853.1
> >
> > I think they should be normalized. Also I checked the idf file and there
> is
> > not indication about the method about normalization. So is there any
> method
> > applicable to eset?
> >
> > Thanks.
> >
> > Zhe
> >
> > -----Original Message-----
> > From: Alex Gutteridge [mailto:alexg@ruggedtextile.com]
> > Sent: 05 August 2010 15:59
> > To: Zhe Liu
> > Cc: bioconductor@stat.math.ethz.ch
> > Subject: Re: [BioC] loading processed data into eset class
> >
> > On Thu, 5 Aug 2010 15:11:34 +0100, "Zhe Liu" <zhliu.tju@gmail.com>
> wrote:
> >> I have a problem with loading matrix data into eset class object. The
> >> data.frame is used to load tab-delimited processed data. But when I want
> > to
> >> run rma() method, there is always a error.
> >>
> >> Eset=new("ExpressionSet", phenoData=phenoData, featureData=featureData,
> >> experimentData=experimentData, exprs=as.matrix(arraydata_pro))
> >>
> >> rEset=rma(Eset)
> >>
> >> when I run the final line, it reported:
> >>
> >> Error in function (classes, fdef, mtable)  :
> >>
> >> unable to find an inherited method for function "probeNames", for
> > signature
> >> "ExpressionSet"
> >
> > rma() works on AffyBatch objects and creates ExpressionSet objects -
> hence
> > the error.
> >
> > If the data is already processed why do you want to run rma?
> >
> > --
> > Alex Gutteridge
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
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> >
>

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