Genes with a value between 100 and 200, i.e. close to background (mean value of 60), or with a crossing point value above 30 by qRT-PCR, were considered to be expressed at low level and are indicated in parentheses.
We applied several filtering steps to discard genes and exons with expression values close to background in an effort to minimize the false positive rate (see Methods).
Moreover, measurements of chemiluminescence after 96 h of in vitro culture of leukocytes showed values close to background signals and differences between fish could no longer be detected (data not shown).
The lower limit of linearity of the dynamic range was around 10 cpc, and the signals reached a bottom plateau with values close to background noise, marking the limit of sensitivity between 1 and 10 cpc.
Briefly, the microarray data were filtered to remove control probe sets and those probe sets with an intensity value close to background levels.
Further, results from SUBarrays were sufficiently reproducible to ensure biological accuracy, though, likely due to higher background and the use of background subtracted intensities, displayed less precision than the Agilent platform, particularly for higher Z score values, where one signal was close to background (Supplementary text S1, Figure S4, S5).
Class 1 represented regions close to background intensities, suggesting a largely DNA-free compartment.
A first description of the expression values showed two problems: censored values and values similar to background values.
After April 15 the scattering values decreased to background values.
Displacement by BaLPS, on the other hand, remained close to the background values obtained with an equal amount of water (Fig. 9A).
