[BioC] estrogen dataset (tif files, before after scanning)

Wolfgang Huber huber at ebi.ac.uk
Wed Jun 1 23:59:38 CEST 2005

Hi Rene,

sorry, I don't have the TIFF files either.

Since you are going to use these data for teaching, I would just like to 
point out that this particular data set is not easy. The time factor has 
  a drastic, transcriptome-wide effect on expression, which probably 
interferes with (or confounds) the normalization. While it is an 
interesting and biology-rich experiment, I am not sure it is the best as 
a textbook example for elementary microarray analysis.

Needless to say that I/we were not aware of this complication when we 
prepared the exercise and it is on my list of things to do to revise it 
and use different set of arrays (but still a 2x2 factorial design).


Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber

Rene Nederhand wrote:

 > Dear list-members,
 > I am looking for the original scans of the 8 Affymetrix micro-arrays
 > that are part of the 2x2 factorial design example described by Robert
 > Gentleman and Wolfgang Huber.
 > I would like to use these in an exercise for a bachelor program
 > bioinformatics. Converting raw tif-images into an expression matrix is
 > part of the exercise. However, this is only possible when the original
 > images and gene-id files are available. Off course, I contacted Robert
 > Gentleman, but he never received those files.
 > Please contact me if you have these files.
 > Kind regards,
 > Rene Nederhand
 > "Sometimes I think the surest sign that intelligent life exists
 > elsewhere is t

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