R Annotations

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annaffy is the package to be concerned with mainly. There's a vignette which shows some of the basics.

Here are some steps I've discovered:

  1. library("annaffy")
  2. library("reposTools")
  3. install.packages2("hgu95av2")
  4. library("hgu95av2") [or library(chipname, character.only = TRUE) ]
  5. probeids <- ls(hgu95av2SYMBOL)
  6. anntable <- aafTableAnn(probeids, "hgu95av2", aaf.handler())
  7. saveText(anntable, "hgu95av2.txt")

Command line parameter handling:

  1. To get the last parameter on the command line - chipname <- commandArgs()[length(args)]

Command line notes:

  1. cat annotationTemplate.R |sed 's/-chipname-/hgu95av2/'>tempannot.R
  2. wget http://www.bioconductor.org/packages/data/annotation/1.7/bin/windows/contrib/2.2/ -O -|grep -o 'zip">.*[^cdf|probe]_'|sed 's/zip">//'|sed 's/_//' > chiplist.txt
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