[BioC] Present/absent probes on miRNA arrays

Heidi Dvinge heidi at ebi.ac.uk
Sun Jul 13 11:31:00 CEST 2008

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?


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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