Entering edit mode
wrighth
▴
260
@wrighth-3452
Last seen 10.2 years ago
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
