Should I always anticipate the hybridization controls, bioB, bioC, bioD, and cre, to be called as Present?
The four transcripts are added to the hybridization cocktail at staggered concentrations. At 1.5 pM, bioB is at the detection limit for most expression arrays and is anticipated to be called Present at least 70% of the time. In contrast, the other controls should be called Present all of the time, with increasing Signal values (bioC, bioD, and cre, respectively). Absent calls, or relatively low Signal values, indicate a potential problem with the hybridization reaction or subsequent washing and staining steps. Check to see if the hybridization cocktail was prepared correctly, if the recommended hybridization temperature and Fluidics Protocol were used, and make sure the SAPE staining solution did not deteriorate. Other than qualitative calls and Signal values, the 3’/5′ ratio data for these controls are not as informative since they do not relate to the quality of the samples and data.
