Package 'oligo' - Bioconductor

28 paCallsValue2. alpha2: a significance threshold in (alpha1, 0.5);3. tau: a small positive constant;4. ignore.saturated: if TRUE, do the saturation correction described in the paper, with asaturation level of 46000;This function performs the hypothesis test:H0: median(Ri) = tau, corresponding to absence of transcript H1: median(Ri) > tau, correspondingto presence of transcriptwhere Ri = (PMi - MMi) / (PMi + MMi) for each i a probe-pair in the probe-set represented by data.The p-value that is returned estimates the usual quantity:Pr(observing a more "present looking" probe-set than data | data is absent)So that small p-values imply presence while large ones imply absence of transcript. The detectioncall is computed by thresholding the p-value as in:call "P" if p-value < alpha1 call "M" if alpha1