[BioC] how to import mas5 data into expresso (affy package)

[James W. MacDonald]

Hi Manisha,

Manisha Brahmachary wrote:
> Hello,
> 
>  
> 
> I will be be obliged if someone can reply to this query:
> 
>  
> 
> I have a question related to expresso and limma package.
> 
>  
> 
> I have mas5.0 normalized data and I do not have the raw .CEL files.
> 
> I want to use limma on the mas5.0 data to find differentially expressed
> genes. 
> 
>  
> 
> I read in the journal publication "affylmGUI: a graphical user interface for
> linear modeling of single channel microarray data", 
> 
> that in the non-standard way, one can use the normalize raw .CEL files by
> mas5.0 methiod using expresso() function with parameters
> 
> and then storing the result of this procedure in an object called
> NormalizedAffyData will ensure that it is recognized by affylmGUI for the
> purposes of creating plots and
> 
> fitting linear models.
> 
>  
> 
> I created an eSet using my mas5.0 data but it wasnot recognized by
> expresso(), since it is not a affybatchObject.

You don't want to run expresso() on the mas5.0 data. The expresso() 
function is designed to convert probe data to expression values, which 
has already been done by the Affy software.

Instead what you want to do now is to go ahead with limma and do the 
analysis. If your mas5 data are not logged, you will want to do that 
first, but from then you can just use limma. You don't even need to put 
things into an ExpressionSet unless you have meta data that you wish to 
associate, as limma will accept a matrix as input.

Best,

Jim


> 
>  
> 
> Can anyone suggest me how I can import mas5.0 normalized data into expresso,
> so that after I process the data there, I can import it into limma?
> 
>  
> 
>  
> 
> Thanks
> 
> manisha
> 
>  
> 
>  
> 
>  
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623