array_type	dabg_p	rpkm_threshold	gene_exp_threshold	exon_exp_threshold	exon_rpkm_threshold	expression_threshold	perform_alt_analysis	analyze_as_groups	expression_data_format	normalize_feature_exp	normalize_gene_data	avg_all_for_ss	include_raw_data	probability_algorithm	FDR_statistic	batch_effects	marker_finder	visualize_results	run_lineage_profiler	run_goelite
exon	0.05	NA	NA	NA	NA	1	yes	yes	log	NA	NA	constitutive probesets	yes	moderated t-test	Benjamini-Hochberg	no	yes	yes	yes	run immediately
AltMouse	0.75	NA	NA	NA	NA	1	yes	NA	log	NA	NA	NA	yes	moderated t-test	Benjamini-Hochberg	no	yes	yes	yes	run immediately
gene	0.05	NA	NA	NA	NA	1	yes	yes	log	NA	NA	constitutive probesets	yes	moderated t-test	Benjamini-Hochberg	no	yes	yes	yes	run immediately
3'array	NA	NA	NA	NA	NA	NA	NA	NA	log	NA	None	NA	no	moderated t-test	Benjamini-Hochberg	no	yes	yes	yes	run immediately
junction	0.05	NA	NA	NA	NA	1	yes	yes	log	NA	NA	constitutive probesets	yes	moderated t-test	Benjamini-Hochberg	no	yes	yes	yes	run immediately
RNASeq	NA	1	200	5	0.5	5	yes	yes	non-log	RPKM	NA	known exons	no	moderated t-test	Benjamini-Hochberg	no	yes	yes	yes	run immediately