From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] gnu: Add r-sva Date: Fri, 13 Jan 2017 22:51:52 +0100 Message-ID: <87lgueljbb.fsf@elephly.net> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33150) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cS9lc-0006qr-P2 for guix-devel@gnu.org; Fri, 13 Jan 2017 16:52:13 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cS9lX-0002Dl-UZ for guix-devel@gnu.org; Fri, 13 Jan 2017 16:52:12 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:21022) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cS9lX-0002D6-Ks for guix-devel@gnu.org; Fri, 13 Jan 2017 16:52:07 -0500 In-reply-to: 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: Ra Cc: guix-devel Ra writes: > * gnu/packages/bioinformatics.scm (r-sva): New variable. > --- > gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++ > 1 file changed, 35 insertions(+) Thanks for the patch. I tried to apply this but got this error: error: corrupt patch at line 12 Could you resend the patch please? > + (description > + "This package contains functions for removing batch effects and > +other unwanted variation in high-throughput experiment. Specifically, > +the sva package contains functions for the identifying and building > +surrogate variables for high-dimensional data sets. Surrogate variables > +are covariates constructed directly from high-dimensional data (like gene > +expression/RNA sequencing/methylation/brain imaging data) that can be used > +in subsequent analyses to adjust for unknown, unmodeled, or latent sources > +of noise. The sva package can be used to remove artifacts in three ways: > +1. identifying and estimating surrogate variables for unknown sources of > +variation in high-throughput experiments Leek and Storey 2007 PLoS > Genetics, > + 2008 PNAS,2. directly removing known batch effects using ComBat > +Johnson et al. 2007 Biostatistics and 3. removing batch effects with known > +control probes Leek 2014 biorXiv. Removing batch effects and using > surrogate > +variables in differential expression analysis have been shown to reduce > +dependence, stabilize error rate estimates, and improve reproducibility, > +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. > Reviews Genetics.") > + (license license:artistic2.0))) Could you please shorten the description? A paragraph or two would be sufficient. We also don’t need the references to publications. If you decide to keep (a shortened variant of) the enumeration, please use texinfo syntax. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC http://elephly.net