ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design

Severgnini, Marco; Cremonesi, Paola; Consolandi, Clarissa; Caredda, Giada; De Bellis, Gianluca; Castiglioni, Bianca

To assess whether a probe pair was significantly above the background (i.e. was 'present' or not), we performed a one-sided t-test (a = 0.01). At the same time, also the type II error was calculated and 1-b used as the estimate of the power of the statistical test. The null distribution was set as the population of 'Blank' spots (e.g. with no oligonucleotide spotted, n = 6) IFs. Two times the standard deviation of pixel intensities of the same spots was added to obtain a conservative estimate. For each Zip-code, we considered the population of the IFs of all the replicates (n = 4) and tested it for being significantly above the nulldistribution (H 0 : m test = m null ; H 1 : m test > m null ).