Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies

Table 1 Number of probe sets and redundant probe sets used in two-sample t-tests between liver and central nervous system (CNS) cell lines from the GeneLogic dilution dataset.

t-test	Total # PS _a (filtered)	# RPS	% RPS	# unigenes_b	# unigenes for RPS
Liver 1.25 vs. CNS 1.25	7257	1998	27.53	5812	901
Liver 2.5 vs. CNS 2.5	7329	2017	27.52	5871	909
Liver 5.0 vs. CNS 5.0	7755	2224	28.68	6164	998
Liver 7.5 vs. CNS 7.5	7905	2287	28.39	6265	1021
Liver 10.0 vs. CNS 10.0	7456	2092	28.06	5952	940
Liver 20.0 vs. CNS 20.0	7386	2042	27.65	5906	918

Notation: PS represents probe sets, RPS redundant probe sets. The numbers following Liver and CNS represent cRNA concentration.
a. The total # of probe sets in HG-U95A GeneChip is 12,627.
b. Only those with unigene labels were counted.

ISSN: 1471-2105