Hello martin
i know that multtest works..but for it to work correctly i need to create a 
class label right..which am not able to ..i am attching the original txt file 
that i created..it is tab delimited..
ID    disease
GSM469509.CEL    A
GSM469510.CEL    A
GSM469511.CEL    A
GSM469512.CEL    A
GSM469514.CEL    A
GSM469518.CEL    A
GSM469520.CEL    A
GSM469522.CEL    A
GSM469523.CEL    A
GSM469508.CEL    H
GSM469513.CEL    H
GSM469515.CEL    H
GSM469516.CEL    H
GSM469517.CEL    H
GSM469519.CEL    H
GSM469521.CEL    H
A stands for atopic,H for healthy normal
now i want to create a class label..can u help?

peevi





________________________________
From: Martin Morgan <mtmorgan@fhcrc.org>

Cc: bioconductor <bioconductor@stat.math.ethz.ch>
Sent: Sat, December 18, 2010 11:02:23 AM
Subject: Re: [BioC] class label

On 12/18/2010 07:56 AM, Peevi Ijkl wrote:
> Hello 
> ok my phenodata(target.txt) looks something like this
> 
> 1.CEL  A
> 1.CEL  A
> 3.CEL  A    
> 4.CEL  H
> 5.CEL  H
> 6.CEL  H
> 
>  i loaded the above into my R using 
> library(affy)
> library(simpleaffy)
> eset<-read.AnnotatedDataFrame("target.txt", header=T, row.names=1, sep="\t" )
> 
> to view my data:
> pData(eset)
> 
> then i did normalization on it
> 
> Rmaeset<-rma(eset)
> 
> now i want to perform multtest..but first i have to create class label..can 
> anyone tell me how do i do tht??

Hi peevi -- You need to be more helpful to us, and stick with your
original question. Likely the problem is that your pd$Diabetic variable
is not what you think it is, e.g., a factor when you're expecting it to
be a character, or of the wrong length, or ???. But how are we to know?
You have to show it to us. And you can't really say 'multtest doesn't
work', because we know that

  example(multtest)

*does* work. And since even simple emails like this can take five
minutes to write, you have to make it easy for us to see what your
problem might be, so no sense giving us a dozen lines of code -- reduce
your real problem to something that shows what the issue is, in just a
few lines, and nothing more.


Martin

> 
> peevi
> 
> 
> 
>      
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> 
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