Re: [PATCH] gnu: Add r-sva

[Ricardo Wurmus]

Ra <address@hidden> 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