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	avg_all_for_ss	include_raw_data	probability_algorithm	visualize_results	run_lineage_profiler	run_goelite
exon	0.05	NA	NA	NA	NA	1	yes	yes	log	NA	constitutive probesets	yes	moderated t-test	yes	yes	decide later
AltMouse	0.75	NA	NA	NA	NA	1	yes	NA	log	NA	NA	yes	moderated t-test	yes	yes	decide later
gene	0.05	NA	NA	NA	NA	1	yes	yes	log	NA	constitutive probesets	yes	moderated t-test	yes	yes	decide later
3'array	NA	NA	NA	NA	NA	NA	NA	NA	log	NA	NA	yes	moderated t-test	yes	yes	decide later
junction	0.05	NA	NA	NA	NA	1	yes	yes	log	NA	constitutive probesets	yes	moderated t-test	yes	yes	decide later
RNASeq	NA	0.1	10	5	0.1	2	yes	yes	non-log	RPKM	known exons	yes	moderated t-test	yes	yes	decide later