Hi.
On Jan 28, 2008 7:04 AM, Sharon <sharonanandhi at="" gmail.com=""> wrote:
> Dear all,
>
> I have an illumina microarray data in a matrix form, ie. simply a
AVG
> signal. Since I don't have detection p-values and STDERR values, it
is
> difficult for me to make a lumi object. Is it possible to apply RSN
on
> matrix format instead of lumi object?
I don't know the details (assumptions/model/algorithm) for the robust
spline normalization method you're referring to, but fyi there are
several bare-bone and rather generic calibration and normalization
methods that takes matrices and lists in the 'aroma.light' package.
/Henrik
>
> Thanks in advance.
>
> Kind regards,
> Sharon
>
> [[alternative HTML version deleted]]
>
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Hi Sharon,
The "rsn" function in the lumi package accepts either an object of
ExpressionSet class (or inherited class like LumiBatch) or a data
matrix. So
you can directly use it. Please read the help of "rsn" function for
more
details. You can also try other normalization methods in other
packages.
Pan
On 1/29/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at="" stat.math.ethz.ch=""> wrote:
> Message: 6
> Date: Mon, 28 Jan 2008 15:04:08 +0000
> From: Sharon <sharonanandhi at="" gmail.com="">
> Subject: [BioC] Robust Spline Normalization (lumi) - illumina data
> matrix
> To: Bioconductor <bioconductor at="" stat.math.ethz.ch="">
> Message-ID:
> <3709c2370801280704i62c11b6bn5ae79f99ffec20ae at mail.gmail.com>
> Content-Type: text/plain
>
> Dear all,
>
> I have an illumina microarray data in a matrix form, ie. simply a
AVG
> signal. Since I don't have detection p-values and STDERR values, it
is
> difficult for me to make a lumi object. Is it possible to apply RSN
on
> matrix format instead of lumi object?
>
> Thanks in advance.
>
> Kind regards,
> Sharon
>
> [[alternative HTML version deleted]]
>
