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[Bioc-devel] minfi preprocessIllumina Error

2 messages · Dario Strbenac, Kasper Daniel Hansen

Original
Dario Strbenac
# 
Hello,

I have a small recommendation. If the user hasn't explicitly loaded the IlluminaHumanMethylation450kmanifest package, then preprocessIllumina will give an error like :

Error in get(name) : 
  object 'IlluminaHumanMethylation450kmanifest' not found

Since the user isn't using any features of IlluminaHumanMethylation450kmanifest directly (i.e. the package has no methods to manipulate its objects, according to the reference manual), is it better style to have require(IlluminaHumanMethylation450kmanifest) inside of preprocessIllumina ? It might be more streamlined for those users that are newer to R.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
Kasper Daniel Hansen
# 
Hi Dario

Doing something like
  require(getManifest(RGset))
is probably a reasonable idea even though it ends up loading a
package.  It certainly saves typing.  We did not like depending on a
specific package (even though we only have one manifest package at the
moment), because of the chance that Illumina puts out more arrays.

I'll add this to the package reasonably soon, but not immediately.

Kasper

On Tue, Nov 15, 2011 at 6:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au> wrote: