Table 1 |
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|
Variance of replicates |
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|
Pre |
Scaled |
Lowess |
Lowess-tip |
Qspline |
Qspline-tip |
Spatial |
|
|
|
|||||||
|
T cells |
0.140 |
0.062 |
0.062 |
- |
0.057 |
- |
0.056 |
|
HIV |
0.097 |
0.042 |
0.032 |
- |
0.031 |
- |
0.030 |
|
glnA.Cy3 |
0.449 |
0.276 |
0.394 |
0.390 |
0.287 |
0.251 |
0.264 |
|
glnA.Cy5 |
0.643 |
0.634 |
0.553 |
0.539 |
0.389 |
0.326 |
0.366 |
|
gnrA.Cy3 |
0.400 |
0.316 |
0.372 |
0.366 |
0.326 |
0.315 |
0.273 |
|
tnrA.Cy5 |
0.466 |
0.473 |
0.393 |
0.384 |
0.353 |
0.318 |
0.338 |
|
T cells |
- |
55.4 |
55.9 |
- |
59.5 |
- |
60.1 |
|
HIV |
- |
56.5 |
66.9 |
- |
67.9 |
- |
68.8 |
|
glnA.Cy3 |
- |
38.6 |
12.2 |
13.1 |
36.1 |
44.1 |
41.2 |
|
glnA.Cy5 |
- |
1.4 |
14.0 |
16.2 |
39.4 |
49.4 |
43.1 |
|
tnrA.Cy3 |
- |
21.2 |
7.2 |
8.7 |
18.6 |
21.4 |
31.8 |
|
tnrA.Cy5 |
- |
0.0 |
15.6 |
17.5 |
24.1 |
31.6 |
27.4 |
|
|
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|
The top half of the table shows average log-signal variances of oligonucleotide array replicates (T-cell control, HIV-infected) and cDNA array replicates (glnA.Cy3 and tnrA.Cy3 controls, glnA.Cy5 and tnrA.Cy5 mutants) before normalization (pre), after log-signal scaling (scaled), global lowess (lowess), scaled print-tip lowess (lowess-tip), global and tip scaled qspline (qspline, qspline-tip) and spatial gradient normalization (spatial). The percent decrease relative to prenormalized variance is also listed for each method in the lower half of the table. |
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|
Workman et al. Genome Biology 2002 3:research0048.1 doi:10.1186/gb-2002-3-9-research0048 |
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