Tests for differential gene expression using weights in oligonucleotide microarray experiments

BMC Genomics

Table 3 Agreement in probeset selections between our methods and Haslett et al. [16]: Given a chosen number of selected probesets, how many of the probesets selected by GFC were also selected by the methods in this paper (corresponding false discovery rate WBH-FDR)

Summarization Method	Number of probesets selected	$Q_{g}^{0}$	$Q_{g}^{c a l l}$	$Q_{g}^{\exp_{e}}$	$Q_{g}^{b e t a_{e}}$	$Q_{g}^{m e a n p}$	$Q_{g}^{w e}$	$Q_{g}^{L P E}$
MAS5	30^a	10^b (3.6e-06^c)	6 (7.6e-06)	10 (6.2e-04)	10 (4.9e-06)	10 (3.6e-06)	11 (3.6e-06)	17 (2.3e-21)
	50	21 (1.4e-05)	13 (1.6e-05)	25 (2.3e-03)	22 (1.0e-05)	21 (1.2e-05)	22 (7.8e-06)	32 (6.0e-13)
	100	56 (3.5e-05)	40 (1.5e-04)	59 (4.1e-03)	57 (2.2e-05)	56 (2.6e-05)	56 (1.9e-05)	61 (3.3e-09)
	139 (2.3e-03)	94 (1.1e-04)	65 (3.3e-04)	96 (9.2e-03)	95 (8.4e-05)	94 (9.3e-05)	94 (6.1e-05)	76 (4.1e-07)
RMA	30	8^d (1.3e-05)	7 (2.5e-05)	9 (1.9e-03)	8 (7.5e-06)	8 (9.7e-06)	8 (5.6e-06)	20 (1.8e-18)
	50	24 (4.3e-05)	13 (5.0e-05)	26 (3.4e-03)	24 (2.8e-05)	24 (3.2e-05)	24 (2.0e-05)	30 (1.8e-11)
	100	60 (1.4e-04)	42 (3.3e-04)	63 (1.1e-02)	60 (9.8e-05)	60 (1.3e-04)	59 (8.0e-05)	62 (3.5e-07)
	139	85 (2.5e-04)	69 (7.4e-04)	92 (1.9e-02)	92 (2.0e-04)	89 (2.2e-04)	85 (1.5e-04)	77 (2.2e-05)

^a The top 30 probesets were selected by each method.
^b 10 probesets overlapped between the top 30 probesets selected by GFC and the top 30 probesets selected by $Q_{g}^{0}$ , when data were summarized using MAS5.
^c The WBH-FDR for the top 30 probesets selected by $Q_{g}^{0}$ was 3.6e-06.
^d 8 probesets overlapped between the top 30 probesets selected by GFC (data normalized by MAS5) and the top 30 probesets selected by $Q_{g}^{0}$ (data normalized by RMA).
^e Sensitivity parameter ν = 0.05.

ISSN: 1471-2164