Hello,

 

I have taken some effort in comparing GCRMA in ArrayAssist vs
BioConductor in november/december last year. In this process, I
discussed my findings with the ArrayAssist helpdesk. To answer your
question: there IS a difference between ArrayAssist and BioConductor!
This is mainly caused because ArrayAssist still have an older
implementation of GCRMA in their software (one of the first version
available in BioConductor, 1.0 or something; I do not exactly now). For
human chips this gives some small differences that seems to be
rounding-off errors, but for mice (mouse430A and moe430plus2) the
differences are more severe (even on log-scale). As far as I know, the
ArrayAssist developers are familiar with these problems. As a matter of
fact, they promised me to update the GCRMA algorithm to the latest BioC
version. Unfortunately, they did not... This is the reason why I am
discarding ArrayAssist most of the time. I obtain non-exchangable
results.

 

Another additional problem is that the SAME GCRMA implementation in
Bioconductor, running the same R source codes and so forth, give
different results on different platforms. R + GCRMA on windows AND Linux
(both 32 bits intel processors) give identical results, whereas on
Solaris machines small round-off errors seems to be present. These are
really platform dependent, as far as I am aware. I consider this latest
issue not to be very important, but it is nice to know. If someone wants
to comment on this? ...

 

Regards,

 

Dr. Philip de Groot

Wageningen University


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