[BioC] Present/absent probes on miRNA arrays

Mark Cowley m.cowley0 at gmail.com
Mon Jul 14 01:14:26 CEST 2008

Hi Heidi,
Using Agilent miRNA arrays, in the "Gene View" output files, there is  
a binary column called "gIsGeneDetected", which, until I can find  
anything better (i.e., something that isn't a mysterious black box)  
will serve my purposes of Present/Absent calls.
As for Exiqon arrays, I have not come up with a great solution,  
besides the simple filter on an intensity cutoff.


On 13/07/2008, at 7:31 PM, Heidi Dvinge wrote:

> Dear list,
> okay, this is a bit off-topic, but here we go.
> I was wondering whether anyone working with some of the new human  
> miRNA
> microarray platforms (e.g. Invitrogen, Ambion, Exiqon, Agilent) have  
> tried
> to come up with some sort of method for present/absent calls? For  
> example
> based on the intensity of mutated probes sequences or on intensity of
> non-human miRNAs on the arrays.
> This is a slightly tricky issue for these platforms since many miRNA  
> tend
> to be present at very low levels in general. In most cases it's also  
> not
> so important since it's the relative signal between samples that is of
> interest. However, some of these platforms also contain probes for
> potentially novel miRNAs that have typically been "discovered" in- 
> house by
> the manufacturers. They seem fairly reluctant to give out any  
> information
> about these hypothetical miRNAs, but it might be interesting to get at
> least a rough idea of how many of these are actually detected above a
> background/noise level in a given sample.
> Any pointers/idea?
> Thanks
> \Heidi
> ------------<<>>------------
> Heidi Dvinge
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD
> Mail: heidi at ebi.ac.uk
> Phone: +44 (0) 1223 492 561
> ------------<<>>------------
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