Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

BMC Genomics

Table 1 Number and statistical significance of detected AS events using both RNA-seq and array technologies

Expression Threshold	Detected Events	Significant events	FDR for significant
RNASeq
Junction coverage > 6 FPKM	9277	4526	2.7e-4
Junction coverage > 2 FPKM	34,961	13,780	4.7e-4
Junction coverage > 2/3 FPKM	92,986	29,443	7.0e-4
Exon-junction arrays
Signal > 50%	10,114	2385	9.2e-4
Signal > 25%	31,506	6197	1.37e-3
No threshold	92,405	11,761	3.45e-3

for different expression thresholds, default filters are junction coverage greater than 2 FPKM for RNA-seq and probe-set signal greater than top 25% quantile for microarray

ISSN: 1471-2164