[BioC] [OT] compatible preprocessing for Affy and non-Affy
ramasamy at cancer.org.uk
Wed May 23 05:25:52 CEST 2007
[[Apologies in advance since this may be an off topic subject but I have
tried hard without finding any consensus.]]
Problem: I am trying to combine data from Affymetrix platform and
non-Affymetrix platform (most of them two-color technologies) from the
raw data (e.g. CEL, GPR). Therefore I need to find the choice of
"compatible" preprocessing for Affy and non-Affy.
I found 3 studies trying to combine Affy with non-Affy. Irizarry et al
(PMID:15846361) uses RMA for Affy and print-tip normalization with no
background correction. Larkin et al (PMID:15846360) uses Li-Wong for
Affy and LOWESS followed by z-scoring between array subgrids. I am
unclear how Brammler et al (15846362) preprocessed their data (although
one of the supplementary alludes to MAS 5.0 for Affymetrix).
Therefore, I have decided to use RMA for Affy and LOESS normalisation
followed by z-scoring (i.e. zero mean, unit variance) the columns/arrays
for non-Affy platforms.
Question: Can anyone kindly point me to any other papers that tries to
address this question? Can anyone comment/correct me on my decision? Any
other suggestions kindly welcome.
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