A matrix of absolute distances, ignoring differences due to insertion-deletion events (indels) and unresolved base calls, is computed for all analysed pairs from the NW alignments and used to define single linkage clusters for each cutoff value.
To analyze periodicity of calling, the intervals between successive calls were computed.
Cell intensity values and probe detection calls were computed using the AffymetrixGeneChip Operating Software GCOSS).
Gene expression values and presence/absence calls were computed using the Affymetrix Statistical Analysis (MAS5) algorithm.
Expression values and detection calls were computed from raw data by following the procedures outlined for the Affymetrix MAS 5.0 analysis software [ 6].
Cell intensity values and probe detection calls were computed from the raw array data using the Affymetrix GeneChip Operating Software (GCOS).
The call with maximum posterior probability is assigned and then the maximum likelihood estimates of the model parameters, assuming these genotype calls, are computed, including the A allele frequency p j and probability of assay failure z j.
To determine if any locus-specific effect could be detected, the number of loci where any, at least 2 or all replicates provided a call was computed.
For each day of the 49 lunar cycles the sex-difference in call totals was computed, then to each of these lunar days was assigned a number 1 – 29.
The z component of the PSD, called PSD z, was computed in coronal slices and averaged over all the slices.
