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Table 1 Test for cross-hybridization induced differential expression.

From: The impact of quantitative optimization of hybridization conditions on gene expression analysis

Fraction of genes

Temperature Ranking

Z

L

M

H

# 1

# 2

# 3

# 4

# 5

# 6

30%

20%

20%

30%

T 4

T 3

T 2

T 5

T 1

T 6

40%

15%

25%

20%

T 4

T 3

T 2

T 5

T 1

T 6

45%

10%

30%

15%

T 4

T 3

T 2

T 5

T 1

T 6

50%

10%

30%

10%

T 4

T 3

T 5

T 2

T 1

T 6

55%

10%

30%

5%

T 4

T 5

T 3

T 2

T 1

T 6

  1. Possibly confounding effects of cross-hybridization induced differential expression were examined using a Langmuir model of microarray hybridization. Samples of varying properties were considered by selecting different fractions of genes with zero (Z), low (L), medium (M), and high (H) expression levels. Each table row shows results for a different simulation. The obtained ranking robustly identified T4 as the best performing temperature for a wide range of sample properties.