[BioC] MAS5 and GCOC difference to get CEL files

[Delphine Fleury]

Dear all,
I am analyzing affymetrix data ATH1 from the same biological experiment 
(material growth, harvesting and RNA extraction done at the same time in 
the same conditions) but hybridized at 2 different dates (the 2d set 
done 1 year later). So , 12 chips were preprocessed with MAS5 getting 
CEL files and 4 chips with GCOS.
At first, I see that the size of the CEL files are about 11 MB for the 
12 chips and about 5 MB for the 4 last chips. Secondly, the mean signal 
of the 4 last chips is lower than those from the 12 chips (cf boxplots 
before normalization, and AffyPLM). 
Is it possible that the lower signal is related to the preprocessing 
method from GCOS ?
Is there someone who observe the same things ?
Could it be a problem to analyse all chips together ?
Thanks
Delphine


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Delphine Fleury 
DEPARTMENT OF PLANT SYSTEMS BIOLOGY           Fax:32 (0)9 3313809 
GHENT UNIVERSITY/VIB,    Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie         VIB
mailto:defle at psb.ugent.be                  http://www.psb.ugent.be