Hi Anirban,

Please don't take things off-list. We like to think the list archives 
will be useful for people to search.

On 9/14/2011 9:44 AM, ANIRBAN BHAR wrote:
> Hi James,
>
> Thanks for your reply.. I want to have expression matrix from CEL 
> file. My question is : do I need to use rma() or some other method to 
> get the matrix?
You still need to clarify what you want, as this question doesn't mesh 
with your previous question. By definition the results from rma() will 
not be 'raw' expression data, but will have been processed by rma().

So please explain *exactly* what you want. What do you mean by 'get' the 
matrix? What do you mean by 'raw' expression data? What do you mean by 
'expression matrix'? What exactly are you trying to do?

Note that I'm not trying to be difficult here. Depending on what I 
assume you mean, I could come up with multiple answers to your 
questions. If you want to get the right answer, you have to ask the 
question in a manner that removes any need to interpret what you are 
getting at.

Best,

Jim


>
> Best regards,
>
> Anirban
>
> On Wed, Sep 14, 2011 at 3:18 PM, James W. MacDonald 
> <jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu>> wrote:
>
>     Hi Anirban,
>
>     Please define 'retrieve'. When you read the data into an AffyBatch
>     using ReadAffy, you then have the raw expression dataset. What
>     exactly do you want to do with it?
>
>     Best,
>
>     Jim
>
>
>
>
>     On 9/14/2011 6:21 AM, ANIRBAN BHAR wrote:
>
>         Hi all,
>
>         How can I retrieve raw expression dataset from CEL files? I
>         don't want
>         normalized dataset...I have already read the CELL files using
>         the following
>         statements:
>
>
>         library(gcrma)
>         Data<- ReadAffy("file1.CEL")
>
>
>         what would be my next steps?
>
>         Thanks in advance,
>
>         Anirban
>
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>
>     -- 
>     James W. MacDonald, M.S.
>     Biostatistician
>     Douglas Lab
>     University of Michigan
>     Department of Human Genetics
>     5912 Buhl
>     1241 E. Catherine St.
>     Ann Arbor MI 48109-5618
>     734-615-7826 <tel:734-615-7826>
>
>     **********************************************************
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>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 

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