[BioC] frma for Nimblegen arrays?

[Hollis Wright]

Hello, all: two-part question here. We have some expression data from Nimblegen rat arrays that was normalized from our microarray service using the internal RMA process Nimblegen uses in their software. Unfortunately, a few of the arrays had physical defects. We've pulled those from our downstream analysis just to be safe but we're unsure if they were used in the normalization process. We've gone ahead with downstream analysis but I'd also like to make sure we're not running into any issues that were baked into the current normalization, just to be safe. So:

1) Should we be concerned in the first place about whether or not these arrays were included in the normalization process? I can't seem to find out exactly what flavor of RMA variant Nimblegen is using. If it's frma, since the normalizations are precomputed it shouldn't matter if the bad arrays were included, should it?

2) Assuming we should be concerned and renormalize, is this easily possible with frma? We have non-normalized data but we don't have the tiff files, just the calls/pairs/xys files. Is that sufficient? Sorry for the basic questions, I've not done microarray normalization in quite a while and that was all on an Affy platform.

Thanks!

Hollis Wright, PhD
Ojeda Lab, Division of Neuroscience
Oregon Health and Science University