Table 4.

Fold changes and P-values of six randomly selected exons with MEAP, RMA, PLIER and FIRMA

ExonID	MEAP	PLIER	RMA	FIRMA
	P-value, FC	P-value, FC	P-value, FC	P-value, FC
ENSE00001442185	0.0272, 1.7658	0.0278, 1.4750	0.0179, 2.1503	0.0472, 1.8533
ENSE00001628012	0.0422, 0.6100	0.0387, 0.6588	0.0065, 0.5370	0.0139, 0.4833
ENSE00000833461	0.0328, 0.2246	0.1218, 0.6572	0.0075, 0.7272	0.0111, 0.7761
ENSE00000855493	0.0130, 0.2531	0.2772, 0.5612	0.0191, 0.6641	0.0256, 0.6345
ENSE00001382781	0.0043, 2.2765	0.0443, 1.4478	0.0230, 1.5832	0.0132, 1.7690
ENSE00001131505	0.0376, 0.3468	0.0392, 0.6565	0.0324, 0.7334	0.0332, 0.7119

Quantitative exon expression values were generated from the median intensity of corresponding probeset expression values for PLIER, RMA, FIRMA and directly from probe intensities for MEAP. Four differentially expressed exons found by MEAP alone are ENSE00000833461, ENSE00000855493, ENSE00001382781 and ENSE00001131505. The other two exons (ENSE00001442185 and ENSE00001628012) without significant differential expression are found by most of the methods. The threshold defining a significant differentially expressed exon was P < 0.05 and linear-scale fold change more than two. The first column of the bolded values denotes significances (P-values). The bolding refers to exons that were detected by MEAP alone.