[BioC] illumina --> limma?

[Axel Rasche]

Sean Davis wrote:
> 
> 
> On 8/24/06 2:50 PM, "Anand Patel" <acpatel at gmail.com> wrote:
> 
>> Using both mouse and human Sentrix-6 beadarrays, I've managed to
>> normalize the arrays both with the beadarray package and the
>> BeadExplorer package.  However, despite being able to get an exprSet
>> from beadarray and a BeadSummaryList from BeadExplorer, I'm not sure
>> how to go to Limma from there.
>>
>> The exprSet does contain normalized values for all of the arrays, and
>> I can construct a new phenoData, but they're not log-values of
>> expression . . .
> 
>  newExprSet <- oldExprSet  #copy old exprSet for safe-keeping
>  exprs(newExprSet) <- log2(exprs(oldExprSet))   #take log of expression
> values

Maybe it is to mention that for some normalisations, the log-values can 
get negative (i.e. for expression values lower than 1). To proceed you 
can convert the negative values to the smallest positive value. So add 
this line:

exprs(newExprSet)[ exprs(newExprSet) < 0 ] = min(exprs(newExprSet)[ 
exprs(newExprSet) > 0 ])

Good luck,
Axel

> 
> I think that will do it.
> 
> Sean
> 
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-- 
*******************************************
Dipl. Math. ETH Axel Rasche
Max-Planck-Institute for Molecular Genetics
Department Lehrach (Vertebrate Genomics)
Ihnestrasse 63-73
D-14195 Berlin-Dahlem
GERMANY

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