BMC Bioinformatics

Table 3 The mean square errors (MSE) of estimated gene expression levels (up:down = 9:1) for simulated cDNA microarray data with the R-I plots similar to Figure 3.

From: A robust two-way semi-linear model for normalization of cDNA microarray data

Percentage of DEG	Descriptive Statistics
	Method	Mean	Minimum	25% Quantile	Median	75% Quantile	Maximum
1%	OLS	0.0370	0.0116	0.0258	0.0323	0.0410	2.2092
	Huber	0.0248	0.0112	0.0195	0.0223	0.0255	1.7156
	Tukey	0.0238	0.0109	0.0191	0.0217	0.0247	1.5648
	LOWESS	0.0375	0.0119	0.0251	0.0321	0.0419	2.2162
5%	OLS	0.0489	0.0126	0.0265	0.0333	0.0422	1.5836
	Huber	0.0324	0.0110	0.0198	0.0228	0.0263	1.1765
	Tukey	0.0299	0.0108	0.0194	0.0222	0.0254	1.0278
	LOWESS	0.0493	0.0125	0.0255	0.0325	0.0429	1.6134
10%	OLS	0.0692	0.0124	0.0285	0.0359	0.0464	1.6907
	Huber	0.0455	0.0098	0.0210	0.0245	0.0288	1.1667
	Tukey	0.0404	0.0102	0.0204	0.0236	0.0276	1.0175
	LOWESS	0.0692	0.0119	0.0270	0.0349	0.0461	1.6846
20%	OLS	0.0961	0.0137	0.0324	0.0428	0.0570	1.8614
	Huber	0.0632	0.0124	0.0235	0.0282	0.0354	1.2969
	Tukey	0.0547	0.0127	0.0225	0.0266	0.0329	1.0525
	LOWESS	0.0950	0.0154	0.0325	0.0431	0.0580	1.8834
40%	OLS	0.1439	0.0147	0.0493	0.0665	0.1007	2.5021
	Huber	0.0960	0.0134	0.0330	0.0446	0.0673	1.9988
	Tukey	0.0821	0.0136	0.0305	0.0401	0.0602	1.6771
	LOWESS	0.1562	0.0187	0.0832	0.1121	0.1418	3.0480
*70%	OLS	0.1530	0.0138	0.0554	0.1146	0.1882	1.2717
	Huber	0.1040	0.0121	0.0366	0.0791	0.1267	0.9153
	Tukey	0.0901	0.0115	0.0337	0.0700	0.1098	0.7778
	LOWESS	0.4082	0.0350	0.1651	0.3563	0.6331	1.0816

DEG: differentially expressed genes. *: all DEG are up-regulated. OLS: the TW-SLM using the ordinary least squares.
Huber: the robust TW-SLM using Huber's weight function. Tukey: the robust TW-SLM using Tukey's weight function.

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ISSN: 1471-2105

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