[BioC] RMA normalisation in Affy

[Ben Bolstad]

The commands 

eset <- rma(Data)

and 

eset <- expresso(Data, bgcorrect.method="rma", normalize.method="quantiles",  pmcorrect.method="pmonly",summary.method="medianpolish")

should (in theory) be giving the same expression values. While the
example you mention does appear in the main affy vignette I am not sure
that it is ever presented as being the way to compute RMA expression
values using the expresso function.


Best,

Ben




On Mon, 2007-09-10 at 10:00 +1000, Yogi Sundaravadanam wrote:
> Hello all
> 
>  
> 
> I am pretty new to using Bioconductor packages and R software, and I was
> wondering if you could help please?
> 
>  
> 
> Whats the difference between the following please?
> 
>  
> 
> eset <- rma(Data)
> 
> and 
> 
> eset <- expresso(Data, normalize.method="qspline",
> bgcorrect.method="rma", 
> 
>                                   pmcorrect.method="pmonly",
> summary.method="liwong") 
> 
>  
> 
> 
> 
> if rma does background corrections, normalises using quantile
> normalisation, and calculates expresssion measure using median polish
> (assuming that is what rma does), are the above two commands just the
> same? 
> 
>  
> 
> Also, in the Affy package documentation,  is the following line an
> errata?
> 
> eset <- expresso(affybatch, normalize.method="qspline",
> bg.method="rma",pmcorrect.method="pmonly",summary.method="liwong"
> 
> I cant seem to find documentation for bg.method? 
> 
>  
> 
> Thanks heaps
> 
> Yogi 
> 
>  
> 
>   _____  
> 
> Yoganand Sundaravadanam
> Bioinformatics Officer
> 
> Australian Genome Research Facility Ltd
>  Email: yogi.sundaravadanam at agrf.org.au
> Web: www.agrf.org.au
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