[BioC] Problem in running affy package

[Chao-Jen Wong]

Hi, Priyanka

The reason that "est<-rma(Data)" works is because function rma returns an "ExpressionSet" instance (see ?rma), and function write.exprs is an ExpressionSet-specific method (see ?write.exprs or showMethods("write.exprs")). On the other hand, the "normalize.AffyBatch.quantiles" function returns an "AffyBatch" instance, and of course "write.exprs" cannot be dispatched to the a method that supports "AffyBatch" instances. 

Chao-Jen


On 03/26/10 23:40, 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 normalizing the data using quantiles method, using following
> command:
>
>   
>> nor<-normalize.AffyBatch.quantiles(Data)
>>     
> The above command is running without any problem.But when i am trying to
> write the normalized file to a new file named"normalized"by the command
> given below, it is showing the following error.
>
>   
>> write.exprs(nor,file="normalized")
>>     
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "write.exprs", for
> signature "AffyBatch"
>
>
> Please try to solve this problem as early as possible.
>
>
> With Regards,
> Priyanka Jain
>
> 	[[alternative HTML version deleted]]
>
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>   


-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M1-B514
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org