Hi Ricardo, On Fri, Jan 13, 2017 at 10:52 PM Ricardo Wurmus <rek...@elephly.net> wrote:
> Ra <ilpuccio.f...@gmail.com> 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.
>
>
follows the patch with the reduced description, sorry for the long version.
I do not know why you get the "corrupt" message, I hope that attaching the
patch file could solve the issue.
* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index d82b6c0..867a72e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,29 @@ immunoprecipitation and target enrichment on small
gene panels. Thereby,
CopywriteR constitutes a widely applicable alternative to available copy
number detection tools.")
(license license:gpl2)))
+
+(define-public r-sva
+ (package
+ (name "r-sva")
+ (version "3.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sva" version))
+ (sha256
+ (base32
+ "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-genefilter" ,r-genefilter)))
+ (home-page "http://bioconductor.org/packages/sva";)
+ (synopsis "Surrogate variable analysis")
+ (description
+ "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. The package
+contains functions for 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.")
+ (license license:artistic2.0)))
--
1.9.1
0001-gnu-Add-r-sva.patch
Description: Binary data
