[BioC] loading processed data into eset class

[Zhe Liu]

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 at ruggedtextile.com] 
Sent: 05 August 2010 15:59
To: Zhe Liu
Cc: bioconductor at 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 at 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