Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA

Table 2 Distance metrics associated with probe set sensitivity to F/T RNA degradation. Probe sets were classified as invariant (INV) to degradation or as decreasing in signal (DEC) in response to degradation. DEC probe sets were further divided into two classes based on probe set location relative to the corresponding reference sequence termini.

Distance metric	INV	DEC	DEC (5'-3' < 1000)	DEC (5'-3' > 1000)
5'-3' distance	638 ± 386	1381 ± 665^a	646 ± 171	1637 ± 576^b
3'-3' distance	211 ± 388	973 ± 653^a	289 ± 228	1212 ± 579^b
5'-5' distance	1072 ± 783	904 ± 764	1250 ± 874	784 ± 689
RefSeq length	1711 ± 845	2285 ± 901^a	1896 ± 830	2420 ± 891^b
TargetSeq length	479 ± 72	451 ± 109	406 ± 111^c	467 ± 105
TargetSeq/RefSeq	0.37 ± 0.21	0.22 ± 0.10^a	0.25 ± 0.14^c	0.21 ± 0.08^b
Avg log₂ RIN 9.5 signal	11.5 ± 1.3	10.0 ± 1.7^a	10.0 ± 1.7^c	10.1 ± 1.8^b
Count	61	89	23	66

ISSN: 1472-6750