[BioC] SE using RMA

Laurent Gautier laurent at cbs.dtu.dk
Wed Apr 9 04:54:19 MEST 2003

On Tue, Apr 08, 2003 at 09:31:19AM -0300, Christian M. Probst wrote:
> c) What are the main implementations in Affy 1.2.9?

You may refer to the file NEWS, found in the root of the package
(although you may have to uncompress the pack you download to see it).
I am not sure about how many new other things will come up, but probably
not so many this time. We are working on cleaning the code and fixing the

For reference, this file currently contains:

Version 1.2 [under development]:

  o Autoload of cdfenvs on demand [almost done. The packages directory
  on the website should be set to be a repository]

  o slot 'preprocessing' of the MIAME attribute used to store
  normalization step information [not finished, list returned
  "constant" and "invariantset" for the moment. Need for a class
  and check compliance with MIAME standards]
  o default methods for normalization, bg correction, pm correction
  and summary now in the package options [options exist for all, but
  only used by normalize for the moment].

  o tuning of the MAS5.0 methods implemented (bgcorrect.mas, ...)
  [Ben for details. add URL for the comparison he made]

  o method plot.ProbeSet, an alternative to barplot, to plot probe
  level information.

  o parameter 'scale' in the method barplot for ProbeSet. All the
  barplots are scaled to eachothers.

  o bug in the parser fixed (infinite loop reported with apparently
  non-standard CEL files).

  o bug in the parser fixed (the 'sd' data returned were not correct).

  o missing slot in the dataset SpikeIn fixed.

Hopin' it helps,


currently at the National Yang-Ming University in Taipei, Taiwan
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

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