Mean ± SEM | p value | |
---|---|---|
Noise | 6.34 ± 0.13 | 0.7 |
RawQ | 3.52 ± 0.06 | 0.792 |
SF | 1.03 ± 0.02 | 0.522 |
GAPDH (3′/5′) | 1.23 ± 0.01 | 0.126 |
260:280 | 1.69 ± 0.02 | 0.554 |
RNA (μg/μl) | 0.51 ± 0.01 | 0.143 |
28S:18S | 1.34 ± 0.01 | 0.38 |
cRNA (μg) | 81.81 ± 1.38 | 0.374 |
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.