A weighted average difference method for detecting differentially expressed genes from microarray data

Table 5 Average number of genes common to each pair of methods for Datasets 3–38

(a) MAS	AD	FC	RP	modT	samT	shrinkT	ibmT
WAD	52.0	39.1	49.7	37.7	45.2	39.8	42.8
AD		61.9	84.1	34.4	47.1	37.2	33.2
FC			58.2	29.5	39.1	31.2	28.1
RP				30.5	41.8	32.4	29.8
modT					79.9	92.7	78.1
samT						83.5	65.0
shrinkT							74.8
(b) RMA	AD	FC	RP	modT	samT	shrinkT	ibmT
WAD	62.2	50.4	60.2	31.7	32.6	30.8	33.4
AD		78.8	84.7	35.2	36.2	33.9	38.0
FC			72.3	32.2	32.8	30.8	34.5
RP				36.8	37.6	35.4	39.4
modT					88.3	93.0	88.4
samT						87.6	83.6
shrinkT							85.1
(c) DFW	AD	FC	RP	modT	samT	shrinkT	ibmT
WAD	84.3	83.9	72.1	13.6	13.4	14.6	13.9
AD		98.6	77.3	13.7	13.5	14.7	14.0
FC			77.0	13.6	13.4	14.6	13.9
RP				18.1	17.9	20.1	18.8
modT					94.1	83.2	93.4
samT						81.1	91.0
shrinkT							83.0

The averages were calculated from top 100 genes. Due to the symmetric nature of the matrix only the upper triangular part is presented.

ISSN: 1748-7188