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

BMC Bioinformatics

Table 3 Average Spearman's correlations between MA and qRT-PCR detection of differentially expressed genes

		MAS5	PLIER	MBEImm	GC-RMA	RMA	MBEI
new annotation	A	71 ± 19	77 ± 9	80 ± 14	82 ± 9	74 ± 17	71 ± 15
	N	71 ± 19	77 ± 9	81 ± 14	82 ± 9	74 ± 17	71 ± 15
	D	74 ± 8	73 ± 15	82 ± 10	82 ± 8	75 ± 13	70 ± 13
	F	73 ± 20	83 ± 9	81 ± 13	84 ± 10	79 ± 19	79 ± 13
	FN	73 ± 20	83 ± 10	81 ± 14	84 ± 10	79 ± 19	79 ± 13
	FD	75 ± 15	77 ± 15	84 ± 13	80 ± 11	77 ± 16	74 ± 10
old annotation	A	70 ± 20	76 ± 11	78 ± 16	81 ± 12	76 ± 14	70 ± 15
	N	70 ± 21	77 ± 11	79 ± 15	80 ± 14	76 ± 15	72 ± 15
	D	75 ± 8	74 ± 14	82 ± 11	74 ± 14	74 ± 14	69 ± 15
	F	72 ± 22	82 ± 10	78 ± 15	81 ± 13	79 ± 14	78 ± 16
	FN	72 ± 22	83 ± 9	79 ± 14	81 ± 15	79 ± 15	80 ± 15
	FD	77 ± 13	77 ± 15	84 ± 14	77 ± 16	77 ± 16	71 ± 13

The table contains mean values and the corresponding standard deviations of Spearman's correlation coefficients calculated for 6 experiments. Correlations were computed between values of Welch's t-statistic 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