[BioC] normalization for custom chip

[Deng, Shibing]

Hi,
We are designing a custom Affymetrix chip with about 1700 genes. By design,
a large number of genes on the chip will be differentially expressed between
our treatment and control samples. The assumption for quantile normalization
and other distribution-based normalization methods will not hold for these
chips. To normalize them, we plan to put some "house-keeping" genes or
"invariant" genes covering a wide range of intensities on the chip. We are
not sure how many house-keeping genes we should have to get a good
normalization? I will appreciate your input on this issue.

Shibing 


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