Each probe on an array was considered to have a positive signal if the median log2 intensity of its technical replicates was above a detection threshold calculated for that array.
Where multiple genes were arrayed, the whole array was considered a single locus.
The median value of each spot on the array was considered and the probes were filtered to remove quality and factory controls.
If the result of array hybridization was in accordance with that of either ITS or D1/D2 domain sequencing, the identification made by the array was considered to be correct.
35,264 transcripts in monocytes that fulfilled the threshold criteria for expressed genes (a raw expression value of at least 20 in half of all measured array was considered as "expressed") were analyzed by principal component analysis (PCA).
The total recovery of dermatophytes and C. albicans from culture and from confirmed positive results of the array was considered 100% and used for performance evaluation of the array and culture methods.
