Skip to main content

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.

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

Distance metric INV DEC DEC (5'-3' < 1000) DEC (5'-3' > 1000)
5'-3' distance 638 ± 386 1381 ± 665a 646 ± 171 1637 ± 576b
3'-3' distance 211 ± 388 973 ± 653a 289 ± 228 1212 ± 579b
5'-5' distance 1072 ± 783 904 ± 764 1250 ± 874 784 ± 689
RefSeq length 1711 ± 845 2285 ± 901a 1896 ± 830 2420 ± 891b
TargetSeq length 479 ± 72 451 ± 109 406 ± 111c 467 ± 105
TargetSeq/RefSeq 0.37 ± 0.21 0.22 ± 0.10a 0.25 ± 0.14c 0.21 ± 0.08b
Avg log2 RIN 9.5 signal 11.5 ± 1.3 10.0 ± 1.7a 10.0 ± 1.7c 10.1 ± 1.8b
Count 61 89 23 66
  1. aP < 0.0001 in unpaired two-tailed t-test comparisons of INV and DEC sets
  2. bP < 0.001 in a Tukey's post-test comparison of a one-way ANOVA
  3. cP < 0.01 in a Tukey's post-test comparison of a one-way ANOVA