[Arrays] microarray data analysis

Igor Chernukhin via arrays%40net.bio.net (by igorc from essex.ac.uk)
Mon Feb 6 04:42:16 EST 2012

Hi All -
I would greatly appreciate if you give me advice on microarray data
We have a custom tilling microarray from Nimblegen for a newly sequenced
genome of (some) organism. The genome is poorly annotated yet and all
probe annotations are in scaffold coordinates. It is dye-swap array
hybridized with mRNA from two different biological conditions. We have
processed the data with nimblegen commercial RMA software and also have
stats made with limma/vsn2 for each probe: fold difference (pmean), fdr.
The research group who studies this organism wants rather simple answer
like which transcripts are upregulated at which conditions and present
it in a ‘simple’ format. RMA output is not really helpful because it
gives all in scaffold coordinates. However we can see the difference in
probe values corresponding to transcript coordinates (annotated from
currently available gff) and of course it varies within the region from
significant to nonsignificant. Would it be appropriate to calculate the
mean of pmean values for each region corresponding to transcript (or
exons) and give it as the answer? Is there any other way of doing it…?

Many thanks

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