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 ------------<<>>------------

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. cheers, Mark 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 > ------------<<>>------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor