[BioC] FARMS package (fwd)

[Günter Klambauer]

Dear Som,

     Of course you can use FARMS with alternative CDFs. We always use it 
in that way. Because of the increase in performance it has made even its 
way into the standard processing pipelines of some pharma companies!

Here is an example for the HuGene11stv1 array:


install either these packages (Linux)

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.download/hugene11stv1hsentrezgcdf_15.0.0.tar.gz
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.download/hugene11stv1hsentrezgprobe_15.0.0.tar.gz
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.download/hugene11stv1hsentrezg.db_15.0.0.tar.gz

or these packages (Windows)

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.download/hugene11stv1hsentrezgcdf_15.0.0.zip
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.download/hugene11stv1hsentrezgprobe_15.0.0.zip
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.0.0/entrezg.download/hugene11stv1hsentrezg.db_15.0.0.zip


specify at reading in:

require(affy)
require(farms)
rawdata <- ReadAffy(filenames=list.files(), cdfname="hugene11stv1hsentrezg")
expressionData <- qFarms(rawdata)

specify cdf later:

require(affy)
require(farms)
rawdata <- ReadAffy(filenames=list.files())
rawdata at cdfName <- "hugene11stv1hsentrezg"
annotation(rawdata) <- "hugene11stv1hsentrezg"
expressionData <- qFarms(rawdata)


Regards,
Günter Klambauer


On 07/30/2012 09:56 AM, hochreit wrote:
>
>
>
>
> ---------- Forwarded message ----------
> From: "hochreit" <hochreit at bioinf.jku.at>
> To: "okko clevert" <okko at clevert.de>, "andi mitterecker"
> <mitterecker at bioinf.jku.at>
> Subject: [BioC] FARMS package (fwd)
> Date: Thu, 19 Jul 2012 15:15:51 +0200
>
>


>
> ---------- Forwarded message ----------
> Message-ID: <SNT108-W5716DB1D77CB762ACBB689CDD90 at phx.gbl>
> From: somnath bandyopadhyay <genome1976 at hotmail.com>
> To: <bioconductor at r-project.org>
> Date: Thu, 19 Jul 2012 06:14:28 -0400
> Subject: [BioC] FARMS package
>
> Hi,
> I was wondering if there is a way of using alternative CDF 
> (brainarray) and PLIER normalization in the FARMS (Factor Analysis for 
> Robust Microarray Summarization) package. I want to further use the 
> I/NI filter to retain informative probesets. Any help would be 
> appreciated.
> Thanks,Som.
>     [[alternative HTML version deleted]]
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