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

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