Skip to main content

Table 2 P-values for evidence for overrepresentation in the functions listed for each method

From: Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity

Functions

A

B

C

D

E

Cancer

7.72E-29

NA

8.15E-24

NA

3.38E-23

cancer

NA

2.58E-25

NA

2.70E-26

NA

carcinoma

8.64E-37

2.52E-33

1.87E-34

2.87E-32

5.56E-30

colon cancer

1.30E-26

1.19E-36

1.10E-26

1.99E-21

3.29E-21

colon tumor

1.10E-26

4.31E-37

3.65E-27

1.80E-21

7.28E-22

colorectal cancer

2.27E-26

4.74E-29

2.43E-26

1.11E-21

1.98E-23

colorectal tumor

2.28E-26

6.80E-29

2.97E-26

4.67E-22

1.72E-23

digestive organ tumor

2.68E-31

6.82E-32

1.24E-28

7.27E-27

2.72E-29

epithelial tumor

2.16E-38

NA

2.27E-35

NA

1.11E-30

gastrointestinal tract cancer

2.35E-25

2.42E-28

4.00E-24

3.19E-21

5.31E-22

intestinal cancer

2.02E-26

5.77E-29

2.58E-26

1.03E-21

1.55E-23

neoplasia

NA

1.63E-24

NA

1.10E-25

NA

solid tumor

3.31E-35

8.07E-32

6.80E-33

4.65E-31

3.88E-29

tumorigenesis

NA

1.55E-26

NA

3.31E-28

NA

uterine serous papillary cancer

3.46E-21

1.71E-20

8.61E-25

1.26E-22

1.14E-15

  1. A - excluding quality-flagged arrays from the analysis. B - applying SVA to batch corrected data. C - ComBat used to correct for batch and quality. D - Array weights included in the linear model. E - including batch and quality as factors in the linear model.