[BioC] Does the strand of a microarray probe matter?

[Cei Abreu-Goodger]

Hello all,

Related issues have arisen before, where the probe of a particular array 
platform was annotated to a gene on the opposite strand. But I was just 
asked if this even matters, or should it simply be considered a case of 
bad probe design.

Does the protocol for different manufacturer's arrays always produce 
amplified product of both strands for the transcript to be measured? I 
could imagine that protocols that amplify based on poly-A tails would 
tend to produce an anti-sense biased amplification product (older Affy 
arrays?), whereas those based on random priming could produce products 
of both strands (and so the actual strand that is on the array becomes 
meaningless).

Does someone know what is the case in particular for Illumina Beadarrays?

Many thanks,

Cei


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