[BioC] Problem in running expresso command in affy package

[Seth Falcon]

Hi,

Please read the posting guide and provide the list with more information 
about your setup (sessionInfo()) as well as more details on what isn't 
working.  Ideally, try to provide an easily reproducible example perhaps 
using sample data that comes with the packages.

+ seth

On 3/27/10 1:00 AM, Priyanka Jain wrote:
> Hello,
>
>           I am using affy package of Biconductor.I have given raw cel files
> as input for normalization. I have to do background correction and
> normalization of these files.
>
> I am using the following commands:
>
>> library(affy)
>> Data<-ReadAffy()
>> est<-rma(Data)
> Background correcting
> Normalizing
> Calculating Expression
> Warning message:
> package 'hgu133acdf' was built under R version c(2, 0, 0) and help will not
> work correctly
> Please re-install it
> S4'
>> write.exprs(est,file="backgroud_corrected")
>
> Till here the raw cel file is being background corrected without any error.
>
> But when i am using expresso command
>
>> normalized<-expresso(Data,normalize.method="qspline",bgcorrect.method="rma",pmcorrect.method="pmonly",summary.method="liwong")
>> write.exprs(normalize, file="normalize_using_expresso")
>
>
> using expresso command the file is not being normalized.
>
> Please try to solve this problem as early as possible.
>
>
> With Regards,
> Priyanka Jain
>
> 	[[alternative HTML version deleted]]
>
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-- 
Seth Falcon
Bioconductor Core Team | FHCRC