Table 1.

Quality control measures

Mean ± SEMp value
Noise6.34 ± 0.130.7
RawQ3.52 ± 0.060.792
SF1.03 ± 0.020.522
GAPDH (3′/5′)1.23 ± 0.010.126
260:2801.69 ± 0.020.554
RNA (μg/μl)0.51 ± 0.010.143
28S:18S1.34 ± 0.010.38
cRNA (μg)81.81 ± 1.380.374
  • Columns: measure, quality control/chip performance; average ± SEM for all 78 chips (because none were significant, results are not broken out according to treatment group); p value for one-way ANOVA across eight groups (n = 9–10 per group). Rows: Noise and RawQ, Affymetrix MAS5-derived measures of overall chip noise and noise among background pixels, respectively; SF, scaling factor, multiplier used to artificially set each chip to a target intensity of 500; GAPDH (3′/5′), on-chip measure of the ratio of signal intensities for the 3′ and 5′ ends of the ″housekeeping″ gene glyceraldehyde-3-phosphate dehydrogenase; 260:280, ratio of the spectrophotometric absorbance at 260 (nucleic acid) and 280 (protein) nm wavelengths; μg/μl RNA, RNA concentration (in ∼22 μl volume) extracted per hippocampus; 28S:18S, Agilent Technologies (Palo Alo, CA) Bioanalyzer 2100 measured ratios of ribosomal RNA (values close to 1 indicate little to no degradation of RNA); cRNA, total μg labeled RNA generated from 8 μg of tissue RNA.