A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

Esnaola, Mikel; Puig, Pedro; Gonzalez, David; Castelo, Robert; Gonzalez, Juan R

doi:10.1186/1471-2105-14-254

Table 2 Mean squared error of false discovery rates under constant library factors

From: A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

#DE	Rank	1.5-fold change		2-fold change		4-fold change
		MSE	Method	MSE	Method	MSE	Method
	1	0.050	DESeq - Pmax	0.050	DESeq - Pmax	0.031	tweeDEseq
	2	0.122	tweeDEseq	0.053	tweeDEseq	0.037	DESeq - Cmax
	3	0.155	DESeq - Cmax	0.065	DESeq - Cmax	0.070	DESeq - Pmax
	4	0.257	DESeq - PgOn	0.104	DESeq - PgOn	0.072	DESeq - PgOn
100	5	0.306	edgeR - QLF Df1	0.138	edgeR - QLF Df1	0.430	edgeR - QLF Df1
	6	0.313	edgeR - QLF (def)	0.177	edgeR - QLF (def)	0.452	edgeR - QLF (def)
	7	0.558	edgeR - (def)	0.336	edgeR - (def)	0.790	edgeR - (def)
	8	0.755	edgeR - Df1	0.431	edgeR - Df1	0.957	edgeR - Df1
	9	9.688	DESeq - CgOn	6.232	DESeq - CgOn	5.133	DESeq - CgOn
	1	0.008	tweeDEseq	0.004	tweeDEseq	0.004	tweeDEseq
	2	0.008	DESeq - Cmax	0.008	DESeq - PgOn	0.007	DESeq - PgOn
	3	0.016	DESeq - PgOn	0.015	DESeq - Cmax	0.014	DESeq - Cmax
	4	0.043	edgeR - QLF Df1	0.087	DESeq - Pmax	0.081	DESeq - Pmax
1000	5	0.045	edgeR - QLF (def)	0.413	edgeR - QLF (def)	0.429	DESeq - CgOn
	6	0.082	DESeq - Pmax	0.459	edgeR - QLF Df1	21.358	edgeR - QLF (def)
	7	0.105	edgeR - (def)	0.532	DESeq - CgOn	22.208	edgeR - (def)
	8	0.155	edgeR - Df1	0.639	edgeR - (def)	23.401	edgeR - QLF Df1
	9	0.735	DESeq - CgOn	0.835	edgeR - Df1	25.004	edgeR - Df1
	1	0.002	DESeq - PgOn	0.001	DESeq - PgOn	0.000	DESeq - PgOn
	2	0.002	tweeDEseq	0.001	tweeDEseq	0.001	tweeDEseq
	3	0.025	DESeq - Cmax	0.031	DESeq - Cmax	0.036	DESeq - Cmax
	4	0.053	edgeR - QLF (def)	0.090	DESeq - Pmax	0.093	DESeq - Pmax
2000	5	0.056	edgeR - QLF Df1	0.183	DESeq - CgOn	0.140	DESeq - CgOn
	6	0.093	DESeq - Pmax	1.444	edgeR - QLF (def)	34.551	edgeR - QLF (def)
	7	0.113	edgeR - (def)	1.702	edgeR - QLF Df1	35.365	edgeR - (def)
	8	0.169	edgeR - Df1	1.724	edgeR - (def)	35.468	edgeR - QLF Df1
	9	0.271	DESeq - CgOn	2.219	edgeR - Df1	36.929	edgeR - Df1

Data in this table correspond to the mean squared error (MSE) values between the empirical false discovery rates (eFDR) and the nominal q-values obtained from the simulation study shown in Figure 7 in which library factors were held constant.

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ISSN: 1471-2105

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