[BioC] chips A,B and C

[James MacDonald]

Technically you are probably correct; the results for a particular gene
may be different if you run rma on the three chip types separately or if
you made a big AffyBatch with all three and ran rma once.

However, this doesn't matter. The expression value for a given gene on
a given chip only makes sense in comparison to the expression value of
the same gene on a different chip (of the same type). In other words, an
expression value of say, 14.5323 doesn't mean anything without another
expression value to compare it to.  Since the A, B, and C chips don't
contain the same genes you will not be comparing the results from chip A
to chip B. Therefore, it doesn't matter if you run rma thrice or only
once.

Jim



James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Antille,Nicolas,LAUSANNE,NRC-BAS"
<nicolas.antille at rdls.nestle.com> 06/16/03 08:39AM >>>
I'm currently working on an experiment involving chips MG_U74Av2,
MG_U74Bv2 and MG_U74Cv2. The RMA normalization treats every
types of chips separately (only one .CDF file is required). Thus, I
need to perform RMA three times and the result is certainly  
different from the one I would obtained performing RMA on all
data simultaneously (especially for quantile normalization).

Has someone already meet this problem? Are the results between
the two methodolgies very different? More generally, do we observe
differences between chips A, B and C (expression level,
variability,...)?

Thank you very much for your response!

Regards

Nicolas

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