Table 1 Detection of alternatively spliced exons on differentially expressed genes: (A) Human tissue dataset, (B) Colon cancer dataset

PLIER

0.001

13555

10737

>0 6513

>0 559 (8.6%)

<0 5954 (91.4%)

<0 4224

>0 4086 (96.7%)

<0 138 (3.3%)

0.05

37746

26652

>0 16456

>0 1736 (10.5%)

<0 14729 (89.5%)

<0 10187

>0 9641 (94.6%)

<0 573 (5.4%)

RMA

0.001

9433

6033

>0 4381

>0 2485 (56.7%)

<0 1896 (43.3%)

<0 1652

>0 1067 (64.6%)

<0 585 (35.4%)

0.05

31238

18628

>0 12318

>0 7295 (59.2%)

<0 5023 (40.8%)

<0 6310

>0 3575 (56.7%)

<0 2735 (43.3%)

Method

Significance level of AS

# of significant probesets

# of significant probesets located on differentially expressed genes ^b (1)

# of probesets in (1) and with mean gene expression difference (2)

# of probesets in (2) and with and mean NI difference

PLIER

0.001

330

220

>0 200

>0 3 (1.5%)

<0 197 (98.5%)

<0 20

>0 20 (100%)

<0 0 (0%)

0.05

8359

3283

>0 2830

>0 134 (4.7%)

<0 2696 (95.3%)

<0 453

>0 436 (96.2%)

<0 17 (3.8%)

RMA

0.001

230

107

>0 105

>0 35 (33.3%)

<0 70 (66.7%)

<0 2

>0 0(0%)

<0 2 (100%)

0.05

7233

2602

>0 2482

>0 1372 (55.3%)

<0 1110 (44.7%)

<0 120

>0 60 (50%)

<0 60 (50%)