Hello all

 

I am pretty new to using Bioconductor packages and R software, and I was
wondering if you could help please?

 

What’s 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 can’t seem to find documentation for bg.method? 

 

Thanks heaps

Yogi 

 

  _____  

Yoganand Sundaravadanam
Bioinformatics Officer

Australian Genome Research Facility Ltd
 Email: yogi.sundaravadanam@agrf.org.au
Web: www.agrf.org.au
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