[BioC] affy: batch completely confounded with treatment

[Juliet Hannah]

All,

A collaborator has approached me with a situation in which a batch is
completely confounded with treatment for
affy gene expression data.

I am wondering if there is anything reasonable to try? For example,
I'm wondering if anything can be done with
control genes.

Does anyone have any suggestions, pointers to papers, or a template
script? The key feature is, of course, the complete
confounding, so that it seems Combat or SVA are not applicable
(correct me if this is incorrect).

I am looking for a way to use the data to generate hypotheses and make
some guesses
with these limitations.

Thanks,

Juliet