Hi, I am using *beadarray* package to analyse the microRNA expression profiling panels (Illumina, Human, http://www.illumina.com/pages.ilmn?ID=240) beginning from the bead-level TIFF/txt files. First question is about annotation of the probes: the annotation file can be downloaded at http://www.switchtoi.com/annotationfiles.ilmn, which is a tab-delimited file containing annotations of miRNAs. It seems that the column 'Array_Address_Id' is actually the Probe_ID saved in the txt/csv files, which should be used to annotate the probes. Am I right? Another question is the 'Detection' method in *beadarray *package, which tells the probability that the probe are detectable against backgrounds, is not available when I started from the bead level. Then how could I find this threshold out? By looking at the 'AveExprs' column with 'topTable' method I am not sure what value I should take. Thank you for your help, Yours, David -- Cheers, David [[alternative HTML version deleted]]