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Statistics of Affymetrix and Custom CDF Files (Version 9)

Table 1: Probe utilization

Species	Chip	Probe count	UG (%)	REFSEQ (%)	ENTREZG (%)	ENSG (%)	ENST (%)	ENSE (%)	VEGAG (%)	VEGAT (%)	VEGAE (%)	TAIR (%)
Arabidopsis thaliana	AtGenome	130858	NA	89.3	NA	NA	NA	NA	NA	NA	NA	89.4
Arabidopsis thaliana	AtH1	250103	NA	90.5	NA	NA	NA	NA	NA	NA	NA	90.9
Bos taurus	Bovine	264126	44.2	52.5	44	19.2	26.6	15.6	NA	NA	NA	NA
Canis familiaris	CfCanine2	471650	29.4	2.2	50.9	46.6	53.2	38.9	NA	.1	NA	NA
Drosophila melanogaster	DmDrosophila2	262766	76	76.3	NA	73.9	76.4	72.3	NA	NA	NA	NA
Drosophila melanogaster	DmGenome1	195186	93.2	93.1	NA	93.2	93.2	90.6	NA	NA	NA	NA
Danio rerio	DrZebrafish	248013	42.3	47.9	24.5	25.1	28.1	23.2	NA	15.7	NA	NA
Gallus gallus	GgChicken	422825	48.4	13.8	43.2	37.9	43.3	32.1	NA	NA	NA	NA
Homo sapiens	Hs133A	246799	69.6	72.1	67.7	68	71.3	63.3	62	71.2	58.3	NA
Homo sapiens	Hs133Av2	246799	69.6	72.1	67.7	68	71.3	63.3	62	71.2	58.3	NA
Homo sapiens	Hs133B	248336	51.6	33.7	30.8	33	34.1	31.3	35.4	40.5	33.9	NA
Homo sapiens	Hs133P	603158	57.9	47.9	44.7	46	48.1	43.2	46.3	52.8	44	NA
Homo sapiens	Hs133X	672804	55.9	46	43.3	44.6	46	43.8	45.6	51.2	44.8	NA
Homo sapiens	Hs95Av2	197695	71.6	74.7	70.5	70.5	73.6	68.5	63.7	73.1	62.1	NA
Homo sapiens	HsEx10stv2	5383654	29.6	21.8	21.7	21.9	21.5	21.6	22.4	24.3	22.1	NA
Homo sapiens	HsFocus	97349	77.7	84.8	79.9	78.5	82.2	72.2	68.6	80.1	63.6	NA
Homo sapiens	HsNuGOHs1a520180	264407	69.5	69.5	65.8	69.9	72.8	65.9	60.6	69.6	57.5	NA
Macaca mulatta	Rhesus	667186	8	NA	48.5	36.3	37.1	34.4	NA	NA	NA	NA
Mus musculus	Mm11KsubA	130180	62.5	64	59.5	56.1	58.5	55	18.6	19.3	18.3	NA
Mus musculus	Mm11KsubB	118480	48.5	51.9	45.6	44.7	49.8	43.1	14.2	15.6	13.7	NA
Mus musculus	Mm430	495374	60.3	51.8	47.3	45.9	48.5	42.8	16.8	17.6	16	NA
Mus musculus	Mm430A	248864	71.8	73.2	67.2	65.1	69.2	60.3	21.6	22.8	20.4	NA
Mus musculus	Mouse Genome 430A 2.0	248864	71.8	73.2	67.2	65.1	NA	60.3	21.6	22.8	20.4	NA
Mus musculus	Mm430B	247610	48.6	30.2	27.3	26.5	27.7	25.1	12	12.4	11.6	NA
Mus musculus	Mm74Av1	200641	55.3	56.2	51.4	49.2	52.3	47.5	16.3	17.1	15.9	NA
Mus musculus	Mm74Av2	196670	61.9	64	58.6	56	59.6	54.2	18.6	19.6	18.2	NA
Mus musculus	Mm74Bv2	195808	59	51.1	46.4	44.7	46.6	43.6	17.3	17.8	17	NA
Mus musculus	Mm74Cv2	181474	32.8	20.1	18.8	17.7	18.2	17.4	7.8	8	7.8	NA
Mus musculus	MmEx10stv1	4737634	29.5	22.3	21.4	21.2	21.2	20.9	8.2	8.2	8.1	NA
Mus musculus	MmNuGOMm1a520177	261635	65.1	63.5	58.8	58.5	61.9	54.2	19.1	20	18	NA
Oryza sativa	OsRice	629427	NA	45.8	NA	NA	NA	NA	NA	NA	NA	NA
Pan troglodytes	Hs133A	246799	NA	71.6	50	46.2	49.8	41.6	NA	NA	NA	NA
Pan troglodytes	Hs133Av2	246799	NA	71.6	50	46.2	49.8	41.6	NA	NA	NA	NA
Pan troglodytes	Hs133B	248336	NA	31.2	27.8	20.3	21.7	18.6	NA	NA	NA	NA
Pan troglodytes	Hs133P	603158	NA	46.3	35.3	30.2	32.5	27.4	NA	NA	NA	NA
Pan troglodytes	Hs133X	672804	NA	44.3	34	28.5	30.3	27.6	NA	NA	NA	NA
Pan troglodytes	Hs95Av2	197695	NA	74.1	52.9	48.1	51.4	46.1	NA	NA	NA	NA
Pan troglodytes	HsEx10stv2	5383654	NA	20.3	18.7	16.2	16.4	15.4	NA	NA	NA	NA
Pan troglodytes	HsFocus	97349	NA	85.3	56.2	53.1	57.2	47.1	NA	NA	NA	NA
Pan troglodytes	HsNuGOHs1a520180	264407	NA	66.5	48.9	44.6	48	40.6	NA	NA	NA	NA
Rattus norvegicus	Rn230	341459	61	46.4	40.4	31.8	33.8	28.6	NA	NA	NA	NA
Rattus norvegicus	Rn230A	174526	68.1	61.4	53.7	44	46.7	39.4	NA	NA	NA	NA
Rattus norvegicus	Rn230B	168033	53.5	30.9	26.6	19.2	20.3	17.5	NA	NA	NA	NA
Rattus norvegicus	Rn34A	139137	63.9	64.9	54.8	49	52.8	46.3	NA	NA	NA	NA
Rattus norvegicus	RnEx10stv1	4027776	23.9	22.9	21.5	21.6	21.6	21.3	NA	NA	NA	NA

Table 2. Target Count for Affymetrix and Custom Probe Sets

Species	Chip	Affy-UG1	Affy-ENSG2	Affy-REFSEQ3	UG	REFSEQ	ENTREZG	ENSG	ENST	ENSE	VEGAG	VEGAT	VEGAE	TAIR
Arabidopsis thaliana	AtGenome	1280	NA	7336	NA	8644	NA	NA	NA	NA	NA	NA	NA	7218
Arabidopsis thaliana	AtH1	NA	NA	21684	NA	24462	NA	NA	NA	NA	NA	NA	NA	21074
Bos taurus	Bovine	15843	5260	10373	9454	12189	9460	5376	9139	7636	NA	NA	NA	NA
Canis familiaris	CfCanine2	15449	16612	17002	10965	744	15809	16510	21927	31939	NA	58	NA	NA
Drosophila melanogaster	DmDrosophila2	NA	13636	13648	13018	19250	NA	13529	19099	20479	NA	NA	NA	NA
Drosophila melanogaster	DmGenome1	NA	12169	12208	11817	17559	NA	12215	17377	20475	NA	NA	NA	NA
Danio rerio	DrZebrafish	12517	5458	8575	7066	9146	4505	4776	6203	7491	NA	3052	NA	NA
Gallus gallus	GgChicken	16366	12172	12309	16388	3888	12516	11978	16519	23693	NA	NA	NA	NA
Homo sapiens	Hs133A	12557	11984	13280	11639	17489	12058	11830	23847	22400	11962	39674	27292	NA
Homo sapiens	Hs133Av2	12515	11984	13280	11639	17489	12058	11830	23847	22400	11962	39674	27292	NA
Homo sapiens	Hs133B	12978	6431	10492	9716	8651	6127	6287	11393	10746	7220	19341	14056	NA
Homo sapiens	Hs133P	24003	17322	20483	20077	25040	17637	17209	34120	34700	18645	58419	44439	NA
Homo sapiens	Hs133X	23919	17353	20609	19729	24767	17497	17029	33086	31756	18496	55772	40529	NA
Homo sapiens	Hs95Av2	7705	8297	9077	8038	12197	8206	8069	16079	14911	8140	26491	18081	NA
Homo sapiens	HsEx10stv2	NA	NA	NA	43943	35494	23976	26220	41624	233460	29872	92868	296228	NA
Homo sapiens	HsFocus	7951	7764	8494	7445	11444	7894	7690	14814	12070	7655	24682	14136	NA
Homo sapiens	HsNuGOHs1a520180	NA	NA	NA	16241	22573	16358	17199	29964	26094	16360	45685	28955	NA
Macaca mulatta	Rhesus	NA	NA	NA	3640	NA	16175	13930	23942	29324	NA	NA	NA	NA
Mus musculus	Mm11KsubA	2143	4137	5186	4268	5916	4219	3992	5163	6048	1292	2703	2646	NA
Mus musculus	Mm11KsubB	2506	3063	3544	2696	3964	2789	2763	3713	5488	839	2315	2628	NA
Mus musculus	Mm430	20590	15726	20500	17867	24711	16297	15758	21043	25438	4930	11724	11881	NA
Mus musculus	Mm430A	12925	11885	13568	11929	16672	12152	11714	15724	18765	3506	8596	8431	NA
Mus musculus	Mouse Genome 430A 2.0	12925	11885	13568	11929	16672	12152	11714	NA	18765	3506	8596	8431	NA
Mus musculus	Mm430B	11842	5494	11325	8627	10385	5400	5400	6878	7688	2155	4117	4021	NA
Mus musculus	Mm74Av1	8061	6964	8887	7073	9596	6937	6653	8689	10225	2086	4599	4569	NA
Mus musculus	Mm74Av2	8060	7712	9059	7563	10612	7663	7351	9603	11309	2311	5110	5086	NA
Mus musculus	Mm74Bv2	8322	5562	7818	6649	9208	5419	5297	6836	7900	1880	3943	3903	NA
Mus musculus	Mm74Cv2	6537	3519	6391	4213	4173	2575	2453	3085	3102	1022	1862	1674	NA
Mus musculus	MmEx10stv1	NA	NA	NA	34107	40873	22659	22761	30067	198575	8721	24685	97583	NA
Mus musculus	MmNuGOMm1a520177	NA	NA	NA	15804	23181	15105	15297	18869	20085	4769	9110	8383	NA
Oryza sativa	OsRice	21718	NA	2339	NA	24015	NA	NA	NA	NA	NA	NA	NA	NA
Pan troglodytes	Hs133A	NA	NA	NA	NA	17065	10766	10263	16534	16218	NA	NA	NA	NA
Pan troglodytes	Hs133Av2	NA	NA	NA	NA	17065	10766	10263	16534	16218	NA	NA	NA	NA
Pan troglodytes	Hs133B	NA	NA	NA	NA	7432	6425	5032	7505	7271	NA	NA	NA	NA
Pan troglodytes	Hs133P	NA	NA	NA	NA	23121	16098	14901	23799	24832	NA	NA	NA	NA
Pan troglodytes	Hs133X	NA	NA	NA	NA	22882	15754	14411	22701	23117	NA	NA	NA	NA
Pan troglodytes	Hs95Av2	NA	NA	NA	NA	11981	7420	6890	10867	11026	NA	NA	NA	NA
Pan troglodytes	HsEx10stv2	NA	NA	NA	NA	24833	24906	20496	31515	173932	NA	NA	NA	NA
Pan troglodytes	HsFocus	NA	NA	NA	NA	11536	6807	6505	9824	8491	NA	NA	NA	NA
Pan troglodytes	HsNuGOHs1a520180	NA	NA	NA	NA	20723	14898	14094	20198	18064	NA	NA	NA	NA
Rattus norvegicus	Rn230	20581	9405	14279	16887	18806	11562	10036	13440	14346	NA	NA	NA	NA
Rattus norvegicus	Rn230A	12406	7102	10490	10413	13277	8678	7545	10068	10255	NA	NA	NA	NA
Rattus norvegicus	Rn230B	11053	3143	6852	8031	7598	3944	3226	4229	4470	NA	NA	NA	NA
Rattus norvegicus	Rn34A	4991	3994	5205	4554	5801	4260	3940	5719	7474	NA	NA	NA	NA
Rattus norvegicus	RnEx10stv1	NA	NA	NA	28596	36744	21334	21920	31616	192301	NA	NA	NA	NA

Table 3. Affy vs Custom

Cdf	Species	Chip	Affy Only	Custom Only	Shared	Percentage of identical probesets in shared targets	Percentage of probesets with difference<=25% in shared targets	Percentage of probesets with difference>50% in all targets
ENSG	Bos taurus	Bovine	1350	1466	3910	20.4	79	44.4
ENSG	Canis familiaris	CfCanine2	1081	979	15531	18.2	78.5	15.5
ENSG	Drosophila melanogaster	DmDrosophila2	286	179	13350	66.6	99	3.5
ENSG	Drosophila melanogaster	DmGenome1	174	220	11995	92.5	99	3.3
ENSG	Danio rerio	DrZebrafish	1283	601	4175	16.4	78.8	34.5
ENSG	Gallus gallus	GgChicken	1181	987	10991	20.7	77.8	19.9
ENSG	Homo sapiens	Hs133A	655	501	11329	42.1	91.1	11.1
ENSG	Homo sapiens	Hs133Av2	655	501	11329	42.1	91.1	11.1
ENSG	Homo sapiens	Hs133B	508	364	5923	50.6	91.2	14.1
ENSG	Homo sapiens	Hs133P	930	817	16392	39	90.4	11.3
ENSG	Homo sapiens	Hs133X	1068	744	16285	49.6	90.6	11.7
ENSG	Homo sapiens	Hs95Av2	516	288	7781	48.3	91	11.3
ENSG	Homo sapiens	HsFocus	423	349	7341	50.3	93.5	10.6
ENSG	Mus musculus	Mm11KsubA	315	170	3822	39.6	87.9	14.5
ENSG	Mus musculus	Mm11KsubB	434	134	2629	19.7	75	24.7
ENSG	Mus musculus	Mm430	853	885	14873	40.7	89.4	12.2
ENSG	Mus musculus	Mm430A	703	532	11182	41.4	90.7	11.6
ENSG	Mus musculus	Mouse Genome 430A 2.0	703	532	11182	41.4	90.7	11.6
ENSG	Mus musculus	Mm430B	546	452	4948	51.6	90	18.3
ENSG	Mus musculus	Mm74Av1	659	348	6305	43	88.1	16.5
ENSG	Mus musculus	Mm74Av2	728	367	6984	38.2	80.8	17.3
ENSG	Mus musculus	Mm74Bv2	526	261	5036	44.9	86.5	16.6
ENSG	Mus musculus	Mm74Cv2	1240	174	2279	37.3	70.3	44.7
ENSG	Rattus norvegicus	Rn230	752	1383	8653	35.5	86.4	22.1
ENSG	Rattus norvegicus	Rn230A	506	949	6596	40.4	90.3	19.7
ENSG	Rattus norvegicus	Rn230B	473	556	2670	34.3	83.3	30.5
ENSG	Rattus norvegicus	Rn34A	345	291	3649	22.7	83	18.2
ENTREZG	Bos taurus	Bovine	2725	1177	8283	30.3	73.1	37.1
ENTREZG	Canis familiaris	CfCanine2	1419	221	15588	17.7	74.4	14.2
ENTREZG	Danio rerio	DrZebrafish	6390	750	3755	15.7	72.7	69
ENTREZG	Gallus gallus	GgChicken	1604	1805	10711	19.4	66.5	30.3
ENTREZG	Homo sapiens	Hs133A	1692	326	11732	37.7	82.2	18.1
ENTREZG	Homo sapiens	Hs133Av2	1692	326	11732	37.7	82.2	18.1
ENTREZG	Homo sapiens	Hs133B	4800	247	5880	35	65.4	51.6
ENTREZG	Homo sapiens	Hs133P	3768	498	17139	25.2	60.6	29.9
ENTREZG	Homo sapiens	Hs133X	4064	533	16964	32.5	62.3	30.9
ENTREZG	Homo sapiens	Hs95Av2	1166	233	7973	44.7	83.7	18.5
ENTREZG	Homo sapiens	HsFocus	815	201	7693	49.5	92.1	12.9
ENTREZG	Mus musculus	Mm11KsubA	1301	146	4073	38.1	84.1	30.5
ENTREZG	Mus musculus	Mm11KsubB	877	97	2692	19.7	71.8	34.3
ENTREZG	Mus musculus	Mm430	6057	366	15931	29.4	65.8	35.7
ENTREZG	Mus musculus	Mm430A	1970	275	11877	37.6	81.1	19.4
ENTREZG	Mus musculus	Mouse Genome 430A 2.0	1970	275	11877	37.6	81.1	19.4
ENTREZG	Mus musculus	Mm430B	7329	167	5233	36.8	66.1	63
ENTREZG	Mus musculus	Mm74Av1	2408	224	6713	38.1	76.3	33.1
ENTREZG	Mus musculus	Mm74Av2	1862	242	7421	36.4	74.5	27.4
ENTREZG	Mus musculus	Mm74Bv2	2909	151	5268	38.8	73.4	42
ENTREZG	Mus musculus	Mm74Cv2	4348	111	2464	30.9	57.8	70.2
ENTREZG	Rattus norvegicus	Rn230	3359	627	10935	29.1	66.8	33.6
ENTREZG	Rattus norvegicus	Rn230A	2308	482	8196	38.2	80.9	28.5
ENTREZG	Rattus norvegicus	Rn230B	3235	326	3618	33.1	69.6	54.3
ENTREZG	Rattus norvegicus	Rn34A	1149	186	4074	22.4	77.3	29.8
REFSEQ	Arabidopsis thaliana	AtGenome	1345	2653	5991	75.5	96.9	40.3
REFSEQ	Arabidopsis thaliana	AtH1	3768	6546	17916	91.3	99	36.7
REFSEQ	Bos taurus	Bovine	1934	3750	8439	51.8	77.7	43.1
REFSEQ	Canis familiaris	CfCanine2	16481	223	521	56.8	72.7	97.1
REFSEQ	Drosophila melanogaster	DmDrosophila2	3370	8972	10278	95.7	98.6	54.7
REFSEQ	Drosophila melanogaster	DmGenome1	3119	8470	9089	93.4	98.7	56.2
REFSEQ	Danio rerio	DrZebrafish	3769	4340	4806	38.4	77.5	66.6
REFSEQ	Gallus gallus	GgChicken	8697	276	3612	52.1	74.3	72.2
REFSEQ	Homo sapiens	Hs133A	4778	8987	8502	56.5	84.8	62.9
REFSEQ	Homo sapiens	Hs133Av2	4778	8987	8502	56.5	84.8	62.9
REFSEQ	Homo sapiens	Hs133B	6088	4247	4404	44.5	68.1	72.4
REFSEQ	Homo sapiens	Hs133P	7803	12360	12680	37.7	63.9	65.1
REFSEQ	Homo sapiens	Hs133X	8071	12229	12538	41.6	65.3	65.6
REFSEQ	Homo sapiens	Hs95Av2	3426	6546	5651	57.9	86.1	65
REFSEQ	Homo sapiens	HsFocus	2990	5940	5504	68.5	93.4	62.4
REFSEQ	Mus musculus	Mm11KsubA	1938	2669	3247	52.3	85.8	60.8
REFSEQ	Mus musculus	Mm11KsubB	1368	1788	2176	40.4	76.2	62.8
REFSEQ	Mus musculus	Mm430	8653	12864	11847	44.1	69.6	66.9
REFSEQ	Mus musculus	Mm430A	4194	7298	9374	58.3	84.6	56.3
REFSEQ	Mus musculus	Mouse Genome 430A 2.0	4194	7298	9374	58.3	84.6	56.3
REFSEQ	Mus musculus	Mm430B	8002	7062	3323	45.5	68.1	83.5
REFSEQ	Mus musculus	Mm74Av1	3511	4220	5376	53.5	79.2	61.2
REFSEQ	Mus musculus	Mm74Av2	3112	4665	5947	50.5	77.3	59
REFSEQ	Mus musculus	Mm74Bv2	4021	5411	3797	46	75.4	73.3
REFSEQ	Mus musculus	Mm74Cv2	4729	2511	1662	32.4	58.8	84.3
REFSEQ	Oryza sativa	OsRice	406	22082	1933	NA	4.3	99
REFSEQ	Rattus norvegicus	Rn230	7347	11874	6932	48	70.8	75.4
REFSEQ	Rattus norvegicus	Rn230A	4734	7521	5756	60.5	83.7	69
REFSEQ	Rattus norvegicus	Rn230B	5363	6109	1489	44.5	73	89.5
REFSEQ	Rattus norvegicus	Rn34A	1776	2372	3429	55.6	83.4	57
UG	Bos taurus	Bovine	7685	1296	8158	50.1	86.2	53.7
UG	Canis familiaris	CfCanine2	6030	1546	9419	37.7	81.5	45.7
UG	Danio rerio	DrZebrafish	6119	668	6398	34	78.1	55.3
UG	Gallus gallus	GgChicken	6438	6460	9928	32.4	76.9	58.6
UG	Homo sapiens	Hs133A	1717	799	10840	43.3	80.9	22.7
UG	Homo sapiens	Hs133Av2	1710	834	10805	43.4	81	23
UG	Homo sapiens	Hs133B	5003	1741	7975	42.1	72.8	50.3
UG	Homo sapiens	Hs133P	6250	2324	17753	35.4	71.1	38.7
UG	Homo sapiens	Hs133X	6433	2243	17486	38.6	70.8	39.5
UG	Homo sapiens	Hs95Av2	1107	1440	6598	46.1	80	32.5
UG	Homo sapiens	HsFocus	1005	499	6946	54.8	90.6	19.7
UG	Mus musculus	Mm11KsubA	521	2646	1622	42.8	80.1	68.9
UG	Mus musculus	Mm11KsubB	569	759	1937	31.5	74.8	46.2
UG	Mus musculus	Mm430	4320	1597	16270	42.6	75.9	32
UG	Mus musculus	Mm430A	1781	785	11144	51.6	83.7	22
UG	Mus musculus	Mouse Genome 430A 2.0	1781	785	11144	51.6	83.7	22
UG	Mus musculus	Mm430B	4429	1214	7413	46	77.3	47
UG	Mus musculus	Mm74Av1	2242	1254	5819	50.4	80.3	41.8
UG	Mus musculus	Mm74Av2	1638	1141	6422	49.3	82.1	34.4
UG	Mus musculus	Mm74Bv2	2449	776	5873	44.7	79.9	39.3
UG	Mus musculus	Mm74Cv2	2987	663	3550	38.9	71.8	55.9
UG	Rattus norvegicus	Rn230	4958	1264	15623	51.1	81.5	31.4
UG	Rattus norvegicus	Rn230A	2660	667	9746	59.4	86.7	27.4
UG	Rattus norvegicus	Rn230B	3741	719	7312	50.7	83	40.4
UG	Rattus norvegicus	Rn34A	1047	610	3944	43.5	78	34.5

1. Identical probe sets are those with identical probe contents in Affymetrix annotation and the custome annotation.
2. Since most probe level data analysis algorithms have built mechanism for dealing with outliers, probe sets that differ only a couple of probes from the Affymetrix probe sets should have similar probe set level signal values.
3. These are probe sets that are supposed to represent the same target but there are >=50% probe content difference between the Affymetrix and custom probe set definition.

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