Tests for differential gene expression using weights in oligonucleotide microarray experiments

BMC Genomics

Table 4 Comparison of our methods and Haslett et al. [16]. Identification of differentially-expressed probesets validated by RT-PCR: given a chosen number of probesets selected by GFC, and the number of probesets validated by RT-PCR within this set, how many of the RT-PCR probesets were selected by the methods in this paper.

Method	# of probesets selected: # of GFC selections validated by RT-PCR	$Q_{g}^{0}$	$Q_{g}^{c a l l}$	$Q_{g}^{\exp_{e}}$	$Q_{g}^{b e t a_{e}}$	$Q_{g}^{m e a n p}$	$Q_{g}^{w e}$	$Q_{g}^{L P E}$
MAS5	30^a : 8^b	5^c	1	5	5	5	5	4
	50 : 11	8	2	7	7	8	7	6
	100 : 12	11	3	10	10	11	10	11
	139 : 13	12	4	11	11	12	12	12
RMA	30 : N/A	2^d	1	4	2	2	2	6
	50 : N/A	6	2	7	6	6	6	7
	100 : N/A	9	4	9	9	9	8	8
	139 : N/A	10	4	11	10	10	10	11

^aThe top 30 probesets were selected by each method.
^b 8 probesets in the top 30 were validated by RT-PCR in Haslett et al. [16].
^c 5 RT-PCR probesets were among the top 30 probesets selected by $Q_{g}^{0}$ . The 5 RT-PCR probesets are among the 8 RT-PCR probesets selected by GFC.
^d 2 RT-PCR probesets were among the top 30 probesets selected by $Q_{g}^{0}$ (data normalized by RMA). The 2 RT-PCR probesets are among the 8 RT-PCR probesets selected by GFC, using the MAS5 normalization.
^e Sensitivity parameter ν = 0.05.

ISSN: 1471-2164