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

Li, Aiguo (NIH/NCI) [E] liai at mail.nih.gov
Mon Jan 5 20:33:52 CET 2009

Dear Henrick,

Wish you had a wonderful holiday season and thank for answering my
questions.  I have two questions to you.

1.  Based on my reading to the information about the aroma.affymetrix,
it is designed for analyzing SNP array data.  Do you think it will be ok
for my case since I need to normalize HG-u133_Plus2 expression array
using dChip with a specific array as median array?

2.  I have created the annotationData/chipTypes/... and
rowData/test_2009/E10252_U133Plus2.cel ... folders.  When I was trying
to run the following script:
cs <- AffymetrixCelSet$byName(name, tags, chipType="HG-U133_Plus_2")
I received a error message saying: "Error in getVector.Arguments(static,
s, length = length, .name = .name) : 
  object "name" not found"
my question to you is that how I can define the name object? As a file
named name 

I appreciate your help!


-----Original Message-----
From: Henrik Bengtsson [mailto:hb at stat.berkeley.edu] 
Sent: Monday, December 29, 2008 10:54 AM
To: Li, Aiguo (NIH/NCI) [E]
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Does any one know a package that allow command line
dChip normalization with a specific median array?


aroma.affymetrix can do this:

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



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
> array as baseline median array.  Does anybody know a package that
> 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
>        [[alternative HTML version deleted]]
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