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 3 Mean squared error of false discovery rates under variable 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	0.030	DESeq - Pmax	0.059	DESeq - Cmax	0.046	tweeDEseq
	2	0.099	tweeDEseq	0.064	tweeDEseq	0.055	DESeq - Pmax
	3	0.189	DESeq - Cmax	0.072	DESeq - Pmax	0.057	DESeq - Cmax
	4	0.194	DESeq - PgOn	0.116	DESeq - PgOn	0.106	DESeq - PgOn
100	5	0.258	edgeR - QLF Df1	0.129	edgeR - QLF Df1	0.124	edgeR - QLF Df1
	6	0.348	edgeR - QLF (def)	0.129	edgeR - QLF (def)	0.153	edgeR - QLF (def)
	7	0.581	edgeR - (def)	0.273	edgeR - (def)	0.290	edgeR - (def)
	8	0.667	edgeR - Df1	0.420	edgeR - Df1	0.380	edgeR - Df1
	9	8.882	DESeq - CgOn	6.429	DESeq - CgOn	5.217	DESeq - CgOn
	1	0.005	tweeDEseq	0.006	tweeDEseq	0.008	tweeDEseq
	2	0.009	DESeq - Cmax	0.012	DESeq - Cmax	0.010	DESeq - Cmax
	3	0.013	DESeq - PgOn	0.012	DESeq - PgOn	0.011	edgeR - QLF Df1
	4	0.016	edgeR - QLF Df1	0.016	edgeR - QLF Df1	0.013	edgeR - QLF (def)
1000	5	0.019	edgeR - QLF (def)	0.017	edgeR - QLF (def)	0.024	DESeq - PgOn
	6	0.054	edgeR - (def)	0.051	edgeR - (def)	0.045	edgeR -(def)
	7	0.083	DESeq - Pmax	0.082	DESeq - Pmax	0.067	DESeq - Pmax
	8	0.087	edgeR - Df1	0.083	edgeR - Df1	0.077	edgeR - Df1
	9	0.700	DESeq - CgOn	0.545	DESeq - CgOn	0.529	DESeq - CgOn
	1	0.003	tweeDEseq	0.004	tweeDEseq	0.005	DESeq - Cmax
	2	0.003	DESeq - PgOn	0.006	edgeR - QLF Df1	0.017	edgeR - QLF (def)
	3	0.006	edgeR - QLF Df1	0.006	edgeR - QLF (def)	0.018	edgeR - QLF Df1
	4	0.007	edgeR - QLF (def)	0.007	DESeq - PgOn	0.023	tweeDEseq
2000	5	0.025	DESeq - Cmax	0.024	DESeq - Cmax	0.029	DESeq - Pmax
	6	0.028	edgeR - (def)	0.026	edgeR - (def)	0.053	edgeR - (def)
	7	0.049	edgeR - Df1	0.047	edgeR - Df1	0.088	edgeR - Df1
	8	0.091	DESeq - Pmax	0.077	DESeq - Pmax	0.092	DESeq - PgOn
	9	0.267	DESeq - CgOn	0.238	DESeq - CgOn	0.465	DESeq - CgOn

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 8 in which library factors were variable.

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ISSN: 1471-2105

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