[BioC] gcrma - all low value output - error somewhere?

[Matthew Hannah]

Hi again,

Now I've used the new gcrma I've noticed something strange, which is
probably an error somewhere, maybe not with gcrma itself.

When I computed gcrma with my old R devel 2.0, BioC devel (gcrma 1.1.1,
ATH1cdf 1.4.3, ATH1probe 1.01, matchprobes 1.0.9, affy 1.5.2) I got
'sensible' expression estimates. Using the current R2.0, BioC 1.5 (all
others above look the same except matchprobes is now 1.0.12 and affy
1.5.8) I get almost all low values - mean ~3 (see graphs). This is the
same if I use justGCRMA() or gcrma(). This isn't due to the
gcrma.bg.transformation file I requested - gcrma(fast=FALSE) now 'works'
(no error) but the values are also low.

I can't think where I'm going wrong as I'm not really typing many
commands. Affy and matchprobes maybe candidates as they are the only
ones with a different version number?

Any ideas?

Thanks,
Matt
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