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

[Henrik Bengtsson]

Hi.

On Mon, Jan 5, 2009 at 8:33 PM, Li, Aiguo (NIH/NCI) [E]
<liai at mail.nih.gov> wrote:
> 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?

No, it is not for SNP chips only.  That's been my main field so it has
naturally methods for those chip types, but as more developers joined
we now support almost all Affymetrix chip types.  Please see the list
of features on the webpage and the vignettes for other examples.

To get exact dChip performance, you'll need to use the dChip software
(http://www.dchip.org/ - note that they have a new forum with links to
Linux ports as well).  I've tried to imitate the dChip normalization
and summarization steps, but I never managed to replicate the results
exactly using R, BioC, etc.

>
> 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

Your setup as written above is not correct.  Pay close attention to
the examples as this is described very carefully and I hope clearly
and unambiguously.  I also recommend you to start reading the User's
Guide:

  http://groups.google.com/group/aroma-affymetrix/web/users-guide

Please post further questions related to aroma.affymetrix to the
aroma.affymetrix mailing list (this is the BioC list).

Cheers

/Henrik

>
> I appreciate your help!
>
> Aiguo
>
> -----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?
>
> 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
>>
>>
>>        [[alternative HTML version deleted]]
>>
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>