[BioC] Number or probes per target. Nimblegen arrays.

[J.delasHeras at ed.ac.uk]

Hi everyone,

not especifically a BioC question this time... but I am hoping to use  
the collective experience regarding a particular array design.

We're considering using human expression arrays from Nimblegen.  
Essentially, we're not sure which format to go for:

1) 6-20 60-mers per target
2) 2-7 60-mers per target

The design #2 uses less probes per target, allowing to have 4 times a  
72k array on one slide (which can be hybridised with separate  
samples), rather than 1 time a 385k array. So it's a smaller array but  
being able to hyb 4 samples in one array reduces costs quite a bit...  
so it's attractive, and my feeling is that it shouldn't be too  
problematic to reduce teh number of probes per gene to this level...  
but it's just a "feeling", having little experience on this type of  
arrays.

Any thoughts about this?

Jose

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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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