Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements

BMC Bioinformatics

Table 4 Average Pearson's correlations between MA and qRT-PCR for estimation of the fold change

		MAS5	PLIER	MBEImm	GC-RMA	RMA	MBEI
new annotation	A	86 ± 11	86 ± 10	89 ± 10	84 ± 9	82 ± 14	81 ± 13
	N	86 ± 11	86 ± 10	89 ± 10	85 ± 10	82 ± 14	81 ± 13
	D	88 ± 9	86 ± 10	88 ± 10	85 ± 7	86 ± 9	81 ± 14
	F	88 ± 11	92 ± 8	90 ± 10	89 ± 10	85 ± 15	85 ± 14
	FN	88 ± 11	92 ± 8	90 ± 10	90 ± 10	85 ± 15	85 ± 14
	FD	90 ± 9	90 ± 9	91 ± 11	89 ± 6	88 ± 9	84 ± 15
old annotation	A	84 ± 13	84 ± 11	88 ± 12	82 ± 11	82 ± 13	79 ± 15
	N	85 ± 13	86 ± 11	89 ± 10	84 ± 11	84 ± 11	81 ± 13
	D	88 ± 9	85 ± 10	86 ± 11	87 ± 9	87 ± 9	80 ± 14
	F	85 ± 13	89 ± 11	88 ± 12	87 ± 13	85 ± 14	83 ± 17
	FN	87 ± 13	91 ± 10	90 ± 10	89 ± 11	87 ± 12	85 ± 14
	FD	90 ± 9	90 ± 9	90 ± 12	88 ± 9	88 ± 9	84 ± 16

The table contains mean values and the corresponding standard deviations of Pearson's correlation coefficients. Correlations were computed between fold changes calculated from MA and qRT-PCR measurements. Columns contain results for the 6 preprocessing algorithms, whereas rows contain results for the 6 filtering/mapping methods (negative signs are removed and values are multiplied by 100) after the new and the old annotations.

ISSN: 1471-2105