Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data

Jones, Lesley; Goldstein, Darlene R; Hughes, Gareth; Strand, Andrew D; Collin, Francois; Dunnett, Stephen B; Kooperberg, Charles; Aragaki, Aaron; Olson, James M; Augood, Sarah J; Faull, Richard LM; Luthi-Carter, Ruth; Moskvina, Valentina; Hodges, Angela K

doi:10.1186/1471-2105-7-211

Table 3 Pre- and post chip variables for samples flagged as potential outliers on at least one post-chip quality control measure. Samples were identified as outliers as judged empirically within the experiment and detailed in the results. Samples (*) were excluded from expression analysis. Samples from cases with prolonged agonal state (†). CB, cerebellum; CN, caudate nucleus; MC, motor cortex.

From: Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data

Pre-chip variables
Sample	PMI		SUBQUAL		RIN		YIELD
H104 CB	14		3		7.4		77
H122 CB*^†	9		2		8.1		68
H85 CB*^†	10		3		7.4		65
HC79 CB*^†	4		4		8.1		44
H123 CN*	7.5		3		7.6		66
HC61 CN	6		3		7.1		59
H131 MC*	13		4		9.1		48
HC71 MC*	5		1		4.3		36
HC52 MC	23		1		6.5		56
HC55 MC	20		1		6.6		44
Post-chip variables: assessed within MAS 5.0 (Affymetrix)
	BG	RAWQ	NOISE	PC_PRESENT		SF	B_ACTIN35		GAPDH35
H104 CB	271	7.5	13.9	42		2.2	1.7		1.2
H122 CB*^†	438	9.5	34.8	36		1.9	1.7		1.0
H85 CB*^†	92	3.6	5.7	49		2.1	1.8		1.1
HC79 CB*^†	87	3.4	5.5	45		1.7	55.9		31.6
H123 CN*	103	3.7	7.6	30		4.1	2.4		0.8
HC61 CN	119	4.0	5.2	43		4.0	1.5		1.2
H131 MC*	250	8.4	38.2	24		1.1	1.6		1.1
HC71 MC*	107	3.6	4.7	26		7.7	4.0		4.1
HC52 MC	122	4.2	6.0	39		3.6	3.9		2.1
HC55 MC	98	3.4	4.7	41		3.4	2.6		2.0
Post-chip variables: assessed within dChip (Li and Wong, 2001)
	DCHIP_AR_OUTLIER		DCHIP_SING_OUTLIER		DCHIP_PCCALL		MEDINT
H104 CB	2.71		0.61		55		597
H122 CB*^†	14.72		1.85		41		1199
H85 CB*^†	6.92		0.40		61		358
HC79 CB*^†	12.75		0.38		55		327
H123 CN*	30.48		1.72		42		369
HC61 CN	4.05		0.58		57		287
H131 MC*	47.59		2.30		36		1620
HC71 MC*	19.66		1.23		39		266
HC52 MC	1.70		0.20		52		331
HC55 MC	3.19		0.29		53		294
Post-chip variables: assessed within Bioconductor packages affy, affyPLM and specialised code [15, 22]
	MED_NUSE	IQR_LR1	B_LR1	IQRplusAbsB_LR1	CV_LR1	IQR_LR2	B_LR2	IQRplusAbsB_LR2	CV_LR2
H104 CB	1.06	0.27	-0.048	0.32	17.3	0.27	-0.029	0.30	10.7
H122 CB*^†	1.24	0.66	-0.105	0.76	16.0	0.64	-0.098	0.74	15.2
H85 CB*^†	1.08	0.42	0.008	0.43	1.9	0.38	0.014	0.40	3.7
HC79 CB*^†	1.12	0.56	-0.001	0.56	0.2	0.56	0.000	0.56	0.1
H123 CN*	1.26	0.67	0.241	0.91	35.9	0.65	0.220	0.87	33.8
HC61 CN	1.06	0.30	0.025	0.33	8.4	0.25	0.000	0.25	0.0
H131 MC*	1.26	1.04	-0.050	1.09	4.8	0.98	-0.040	1.02	4.1
HC71 MC*	1.2	0.96	0.165	1.13	17.2	0.87	0.150	1.02	17.3
HC52 MC	1.06	0.43	0.063	0.49	14.5	0.34	0.039	0.38	11.3
HC55 MC	1.07	0.42	0.039	0.46	9.4	0.34	0.015	0.35	4.4
Post-chip variables: assessed within affy, Bioconductor
	RNADEG_SLOPE					PVAL_SLOPE
H104 CB	2.40					3.8 × 10^-9
H122 CB*^†	0.86					4.9 × 10^-3
H85 CB*^†	2.22					1.2 × 10^-7
HC79 CB*^†	3.96					1.0 × 10^-9
H123 CN*	1.61					3.2 × 10^-7
HC61 CN	2.40					9.7 × 10^-9
H131 MC*	1.17					2.2 × 10^-5
HC71 MC*	2.67					6.0 × 10^-10
HC52 MC	3.61					4.2 × 10^-12
HC55 MC	3.20					3.2 × 10^-11

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ISSN: 1471-2105

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