From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 12/16] gnu: Add r-vsn. Date: Tue, 17 Jan 2017 15:11:37 +0100 Message-ID: <20170117141141.11694-13-rekado@elephly.net> References: <20170117141141.11694-1-rekado@elephly.net> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40269) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTUVD-0007aT-U9 for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:51 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTUV8-0006tP-9L for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:47 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:21003) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cTUV7-0006rf-Vr for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:42 -0500 In-Reply-To: <20170117141141.11694-1-rekado@elephly.net> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * gnu/packages/bioinformatics.scm (r-vsn): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9e073843e..82a60dae0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8330,3 +8330,36 @@ CDF file formats.") "This package contains functions for exploratory oligonucleotide array analysis.") (license license:lgpl2.0+))) + +(define-public r-vsn + (package + (name "r-vsn") + (version "3.42.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "vsn" version)) + (sha256 + (base32 + "0mgl0azys2g90simf8wx6jdwd7gyg3m4pf12n6w6507jixm2cg97")))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-ggplot2" ,r-ggplot2) + ("r-limma" ,r-limma))) + (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html") + (synopsis "Variance stabilization and calibration for microarray data") + (description + "The package implements a method for normalising microarray intensities, +and works for single- and multiple-color arrays. It can also be used for data +from other technologies, as long as they have similar format. The method uses +a robust variant of the maximum-likelihood estimator for an +additive-multiplicative error model and affine calibration. The model +incorporates data calibration step (a.k.a. normalization), a model for the +dependence of the variance on the mean intensity and a variance stabilizing +data transformation. Differences between transformed intensities are +analogous to \"normalized log-ratios\". However, in contrast to the latter, +their variance is independent of the mean, and they are usually more sensitive +and specific in detecting differential transcription.") + (license license:artistic2.0))) -- 2.11.0