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

BMC Bioinformatics

Table 2 Correlation between Microarray and Taqman fold-changes

Transformation Background cor.	GEH S1 r - ICC	GEH S3 r - ICC	EPP S1 r - ICC	EPP S3 r - ICC
Log2
Standard	0.86 - 0.78	0.86 - 0.81	0.84 - 0.72	0.82 - 0.68
No background	0.84 - 0.66	0.84 - 0.68	0.68 - 0.30	0.67 - 0.27
Edwards	0.86 - 0.78	0.86 - 0.82	0.84 - 0.72	0.82 - 0.68
NormExp	0.86 - 0.77	0.86 - 0.79	0.83 - 0.67	0.81 - 0.63
Glog
Standard	0.83 - 0.68	0.83 - 0.70	0.77 - 0.55	0.76 - 0.53
No background	0.81 - 0.60	0.81 - 0.63	0.65 - 0.33	0.65 - 0.30
Edwards	0.83 - 0.68	0.83 - 0.70	0.79 - 0.61	0.77 - 0.59
NormExp	0.83 - 0.67	0.83 - 0.69	0.77 - 0.54	0.77 - 0.61

Product-moment correlation (r) and intraclass Correlation (ICC) between log2 fold-changes obtained with quantitative PCR and log2 fold-changes obtained with microarray.

ISSN: 1471-2105