[BioC] Different gcRMA results depending on platform and version

Sean Davis sdavis2 at mail.nih.gov
Tue Feb 5 20:26:13 CET 2008

On Feb 5, 2008 11:20 AM, JONG-MIN LEE <dungras at gmail.com> wrote:
> Hi, all,
> I just found gcRMA expression values for U133p2 arrays are different
> depending on platform and version.
> I compared two gcRMA expression values and they were quite different.
> The first one was by is R2.6.0, gcRMA 2.10.0, on Unix.
> The second one was obtained by R2.4.0, gcRMA 1.6.0, on WIndows XP.
> So, there was nothing in common between two, and I didn't try to figure out
> whether the difference came form platform difference or version difference
> (R or gcrma).
> Nonetheless, I was expecting consistent results regardless of platform of
> version.

Hi, JongMin.

I cannot comment directly about the differences you are seeing, but I
would not be surprised if there were some changes to R and gcRMA in
the space of 2-3 years that might account for the differences.
Typically, your best bet is to use the most recent version of R and
bioconductor packages whenever possible.


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