Evaluation of normalization methods for cDNA microarray data by k-NN classification

BMC Bioinformatics

Table 5 Leave-one-out cross-validation k-NN error rates for location normalized data. For each data set, the normalization methods were ranked based on their LOOCV classification error rates ("Rank"). The smaller the LOOCV classification error rate, the lower the rank. The methods are arranged in the following order: single-bias-removal methods (block 1), double-bias-removal methods (block 2) and the qspline-related methods (block 3). For a given data set, the smallest error rate(s) and rank(s) are shown in bold. The methods and data sets are described in Tables 1, 2 and 4, respectively.

Location Normalization method	LIVER CANCER		LYMPHOMA		RENAL CELL CARCINOMA		GASTRIC CARCINOMA		LUNG CANCER
	Error Rate	Rank	Error Rate	Rank	Error Rate	Rank	Error Rate	Rank	Error Rate	Rank
N ONRM	0.202	24	0.266	23	0.237	24	0.0347	24	0.359	23.5
GMEDIAN	0.163	21	0.247	21	0.158	22	0.0270	23	0.342	20.5
SL LOESS	0.136	9.5	0.272	24	0.132	16.5	0.0154	12	0.350	22
SL FILTERW3	0.155	16	0.216	20	0.132	16.5	0.0190	14	0.359	23.5
SL FILTERW7	0.144	12.5	0.253	22	0.132	16.5	0.0228	16	0.325	17.5
IG LOESS	0.133	8	0.186	15.5	0.132	16.5	0.0231	20	0.342	20.5
IL LOESS	0.110	2	0.154	13	0.132	16.5	0.0231	20	0.275	12.5
IST SPLINE	0.129	7	0.177	14	0.114	7	0.0153	10	0.334	19
IG SG LOESS	0.136	9.5	0.130	10	0.132	16.5	0	2	0.283	15
IG LOESS-SL LOESS	0.113	3.5	0.117	6.5	0.119	10	0.0154	12	0.242	8.5
IL LOESS-SL LOESS	0.105	1	0.111	4	0.132	16.5	0.0193	15	0.267	10
IG LOESS-LFILTERW3	0.158	19.5	0.136	11	0.092	1.5	0.0231	20	0.242	8.5
IG LOESS-SL FILTERW7	0.113	3.5	0.111	4	0.119	10	0.0154	12	0.217	4
IST SPLINE-SL LOESS	0.121	6	0.102	1	0.119	10	0.0233	22	0.192	1
IST SPLINE-SL FILTERW3	0.157	18	0.139	12	0.092	1.5	0.0229	17.5	0.209	2.5
IIST SPLINE-SL FILTERW7	0.118	5	0.127	9	0.132	16.5	0.0229	17.5	0.209	2.5
Q SPLINEG	0.158	19.5	0.192	17.5	0.096	3.5	0	2	0.275	12.5
QS PLINER	0.166	22	0.123	8	0.096	3.5	0	2	0.275	12.5
Q SPLINEG-SL LOESS	0.138	11	0.198	19	0.119	10	0.00769	7.5	0.225	6
Q SPLINEG-SL FILTERW3	0.144	12.5	0.186	15.5	0.172	23	0.00758	5	0.317	16
Q SPLINEG-SL FILTERW7	0.149	14	0.192	17.5	0.106	6	0.00758	5	0.225	6
QS PLINER-SL LOESS	0.155	16	0.105	2	0.105	5	0.00769	7.5	0.225	6
QS PLINER-SL FILTERW3	0.155	16	0.111	4	0.145	21	0.00758	5	0.325	17.5
QS PLINER-SL FILTERW7	0.169	23	0.117	6.5	0.119	10	0.0114	9	0.275	12.5

ISSN: 1471-2105