[BioC] affylmGUI - feedback, questions

[Steffen Moeller]

Hello,

I just made my first experiences with affylmGUI and am very excited about it. Many thanks for this!

Some questions/comments rather important to me:

* With three different targets, say A (complete vaccine),B (only the adjuvant), C (untreated)
  I am only allowed to enter two contrasts. This is probably
  mathematically fine since the third is not linearly independent of
  the first two, however, for drawing the VennDiagram and the HeatMap,
  I am very iterested to see
	  A-B, A-C and B-C
  which make it three contrasts that apparently I cannot specify in
  affylmgui. What should I do?

* Can I combine target specifications? E.g. A (sick) vs B+C (healthy),
  referring to the A,B,C of above?

* When plotting a heatmap, it is always the first contrast that is used
  as a reference, whatever I contrast I specify in the window.

Some less important issues

* I can extend the window for the TopTable, but the table itself is not
  extended.

* The font size of the Heatmap is not changing with a resize of the
  drawing,

* When selecting gcrma but not having the library gcrma installed, lots
  wish errors pop up, but affylmGUI lists the normalisation as
  available.

* For the report I suggest to help the authors of the paper with a
  methods section that lists references for the methods used, parameters
  and the like. Maybe I can come up with a suggestive patch for
  this. GeneSpring has this feature and I always found this a bit funny -
  it isn't. Amazon would have patented this :-) Btw, the report is
  great!

* Consider to have a window with a log of the R statements required to
  achieve a particular result.

Many greetings and thanks in advance for any help

Steffen

--
  Steffen Moeller, PhD
  University of Rostock
  Institute of Immunology
  moeller at pzr.uni-rostock.de