Hi,

I have been using limma and gcrma for microarray analysis for a while.
recently I have to reinstall my system so I update my R from 2.4 to 2.5.1
I don't know the version of limma,gcrma packages, but they were installed
as I install my old R 2.4.  However, when I run the same script to analyze
the same file I did last year, I got different results for both gcrma and
limma.
Although the difference is not dramatic. I plotted the scatter plot for
gcrma
summarized expression data from old analysis and new analysis, it supposed
to be a straight line, but on my plot the low expression values form a
slightly
 inflated data cloud around the diagonal line. For limma, only about 10
really
large or really small t statistics are strongly different from the old
analysis.
Is this a known issue for using different version of packages ?

Thanks,
Hongqing

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