Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

BMC Bioinformatics

Table 3 Correlation between cumulative Gaussian quantiles of p-values obtained with Taqman and Microarray

Transformation Background cor.	GEH S1 r - ICC	GEH S3 r - ICC	EPP S1 r - ICC	EPP S3 r - ICC
Log2
Standard	0.50 - 0.28	0.49 - 0.36	0.41 - 0.15	0.47 - 0.19
No background	0.52 - 0.45	0.51 - 0.48	0.49 - 0.34	0.48 - 0.24
Edwards	0.50 - 0.27	0.48 - 0.34	0.42 - 0.16	0.49 - 0.22
NormExp	0.50 - 0.30	0.50 - 0.39	0.40 - 0.15	0.48 - 0.14
Glog
Standard	0.52 - 0.46	0.51 - 0.47	0.47 - 0.35	0.51 - 0.36
No background	0.50 - 0.43	0.49 - 0.47	0.47 - 0.34	0.45 - 0.19
Edwards	0.52 - 0.45	0.51 - 0.47	0.45 - 0.32	0.51 - 0.34
NormExp	0.52 - 0.45	0.50 - 0.47	0.48 - 0.38	0.50 - 0.27

Product-moment correlation (r) and intraclass Correlation (ICC) between the cumulative Gaussian quantiles of p-values obtained with quantitative PCR and cumulative Gaussian quantiles of p-values obtained with microarray.

ISSN: 1471-2105