[BioC] Fwd: [devteam-bioc] information about genefilter package

James W. MacDonald jmacdon at uw.edu
Fri Nov 1 20:22:37 CET 2013


Hi Paola,

For a good example, see page 112 in the limma User's Guide:

http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

Best,

Jim

On Friday, November 01, 2013 3:13:52 PM, Hervé Pagès wrote:
> Hi Paola,
>
> I'm forwarding your question to the Bioconductor mailing list where,
> hopefully, someone will be able to help you.
>
> Cheers,
> H.
>
> -------- Original Message --------
> Subject: [devteam-bioc] information about genefilter package
> Date: Sun, 27 Oct 2013 19:58:27 +0100 (CET)
> From: Maintainer <maintainer at bioconductor.org>
> Reply-To: paola.orsini- at libero.it
> To: maintainer at bioconductor.org
>
> Hi,
> I write you to have some  information about genefilter package. I am a
> biologist and a pre-doc student, I must admit that I am quite new to
> microarray
> data analysis and R. I'm analyzing Agilent single color gene
> expression data
> and I'm using limma. I would like to filter my data and to identify the
> detected genes in a % of my samples (something like the "Present"
> call). I
> particular, I want to filter out the genes that have a lower
> expression level
> than the background. I read that genefilter package has several
> methods for
> filtering genes from microarray experiments, but I don't know which
> function of
> the package should I use. Could you give me any information about this?
> Thank  you very much for your support.
>
> Kind regards,
>
> Paola Orsini
>
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099



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