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.
Sean
We did make differences on the gcRMA when we updated from 1.x.x to the
2.x.x versions. Different results are expected because of the change
in
background estimation. However, assessment on the calibration data
(two
latin square datasets) showed that there is not much practical
differences. For two samples, the differences in expression values
from
two different versions of gcrma should still be close to identical.
(For
example, you may see one gene used to be 6 and 6.1 across two samples
and became 5 and 5.1 in another version, but the differences in
expression are both .1).
JONG-MIN LEE 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.
> Has anyone noticed this?
> Thanks.
> JongMIn
>
> [[alternative HTML version deleted]]
>
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--
-------------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI 02912
Tel: 401 863 1230
Fax: 401 863 9182
http://stat.brown.edu/~zwu
