[BioC] Does any one know a package that allow command line dChip normalization with a specific median array?

[Henrik Bengtsson]

Hi,

aroma.affymetrix can do this:

library("aroma.affymetrix");
csR <- AffymetrixCelSet$byName("MyDataSet", chipType="HG-U133_Plus_2");
cfT <- getFile(csR, 14); # Normalize toward array #14 (say)
qn <- QuantileNormalization(csR, targetDistribution=cfT);
csN <- process(qn);

For further question, please join the aroma.affymetrix mailinglist
[http://www.braju.com/R/aroma.affymetrix/].

Cheers

Henrik

On Wed, Dec 24, 2008 at 4:15 PM, Li, Aiguo (NIH/NCI) [E]
<liai at mail.nih.gov> wrote:
> Hello all,
>
>
>
> I need to normalize expression array from command line using a specific
> array as baseline median array.  Does anybody know a package that allows
> me to do that?  I have checked the expresso package and think that it
> does not allow me to specify a specific array as median array.
>
>
>
> Thanks and have great holiday!
>
>
>
> AG Lee
>
>
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