I need to extract expressed gene probe-sets from a microarray control experiment. It is a single GEO dataset, with a single cy3 labelled control sample. I understand that the way to go about this is to set some threshold value (based on the distribution of intensities) and then extract all the probeset ids with values above the threshold value. Any ideas how to go about this ? I would like to implement this in R/Bioconductor, but if there are software packages online that will accomplish this task that would be fine too.
Any help would be much appreciated