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Statistics of Affymetrix and Custom CDF Files (Version 8)

Table 1: Probe utilization

Species Chip Probe count UG (%) REFSEQ (%) ENTREZG (%) ENSG4 (%) ENST4 (%) ENSE4 (%) TIGR (%) TAIR (%)
Arabidopsis thaliana AtGenome 130858 NA 89.3 NA NA NA NA 93.5 89.4
Arabidopsis thaliana AtH1 250103 NA 90.5 NA NA NA NA 93.3 90.9
Canis familiaris CfCanine2 471650 28.2 1.9 50.9 50.2 59.1 42.2 NA NA
Drosophila melanogaster DmDrosophila2 262766 75.1 75.8 NA 73.1 75.6 71.6 NA NA
Drosophila melanogaster DmGenome1 195186 93 93.2 NA 93.1 93.2 90.5 NA NA
Danio rerio DrZebrafish 248013 22.9 40.4 23.3 23.8 28.8 22.1 NA NA
Gallus gallus GgChicken 422825 39.5 12.6 NA 36.6 40.8 30.7 NA NA
Homo sapiens Hs133A 246799 59.4 70.7 66.6 69.7 72.9 65.2 NA NA
Homo sapiens Hs133Av2 246799 59.4 70.7 66.6 69.7 72.9 65.2 NA NA
Homo sapiens Hs133B 248336 45.7 32.4 30.8 37.4 38.6 35.7 NA NA
Homo sapiens Hs133P 603158 50.1 47.1 44.6 49.7 51.8 46.9 NA NA
Homo sapiens Hs133X 672804 47.9 45.1 43.3 48.6 50 47.7 NA NA
Homo sapiens Hs95Av2 197695 62.3 72.9 69.2 71.4 74.5 69.5 NA NA
Homo sapiens HsEx10stv2 5383654 24.8 20.9 21.4 24.9 24.5 24.6 NA NA
Homo sapiens HsFocus 97349 67.2 83.4 78.4 78.5 82.1 72.5 NA NA
Mus musculus Mm11KsubA 130180 62.1 63.1 60 58 60.3 56.9 NA NA
Mus musculus Mm11KsubB 118480 48.5 51.5 45.9 45.6 50.7 44 NA NA
Mus musculus Mm430 495374 59.2 50.7 48.3 49.1 51.7 46 NA NA
Mus musculus Mm430A 248864 71.4 71.9 67.6 67.4 71.4 62.7 NA NA
Mus musculus Mm430B 247610 46.7 29.5 28.9 30.7 31.9 29.3 NA NA
Mus musculus Mm74Av1 200641 55 55 52 50.8 53.9 49.1 NA NA
Mus musculus Mm74Av2 196670 61.5 62.6 59 57.9 61.3 56.1 NA NA
Mus musculus MmEx10stv1 4737634 28.3 22 22.9 23.1 23.1 22.9 NA NA
Oryza sativa OsRice 629427 NA 37.1 NA NA NA NA 74.2 NA
Pan troglodytes Hs133A NA NA NA 14.9 47.6 50.5 43.3 NA NA
Pan troglodytes Hs133Av2 NA NA NA 14.9 47.6 50.5 43.3 NA NA
Pan troglodytes Hs133B NA NA NA 6.4 20.2 21 18.6 NA NA
Pan troglodytes Hs133P NA NA NA 9.9 30.8 32.6 28.2 NA NA
Pan troglodytes Hs133X NA NA NA 8.4 29.5 30.7 28.6 NA NA
Pan troglodytes Hs95Av2 NA NA NA 14.4 50 52.4 48 NA NA
Pan troglodytes HsEx10stv2 NA NA NA 10.9 15.7 15.6 15 NA NA
Pan troglodytes HsFocus NA NA NA 16.8 54.7 58 49 NA NA
Rattus norvegicus Rn230 341459 50.5 47.5 32.8 25.9 27.9 22.8 NA NA
Rattus norvegicus Rn230A 174526 57.7 62.4 45.5 37.4 40.1 32.9 NA NA
Rattus norvegicus Rn230B 168033 42.8 32.1 19.8 13.9 15.1 12.3 NA NA
Rattus norvegicus Rn34A 139137 59 65.5 51.3 46.8 50.6 44.2 NA NA
Rattus norvegicus RnEx10stv1 4027776 16.1 24.1 21.4 20.4 20.4 20.1 NA NA
Vitis vinifera VvGrape 261838 NA NA NA NA NA NA 68.9 NA
 

Table 2. Target Count for Affymetrix and Custom Probe Sets

Species Chip Affy-UG1 Affy-ENSG2 Affy-REFSEQ3 UG REFSEQ ENTREZG ENSG4 ENST4 ENSE4 TIGR TAIR
Arabidopsis thaliana AtGenome 1278 NA 7333 NA 8644 NA NA NA NA 10308 7218
Arabidopsis thaliana AtH1 NA NA 21683 NA 24465 NA NA NA NA 28294 21074
Canis familiaris CfCanine2 12967 18141 16873 10041 643 15861 17287 29346 37422 NA NA
Drosophila melanogaster DmDrosophila2 NA 13272 13680 12985 18982 NA 13387 18850 20116 NA NA
Drosophila melanogaster DmGenome1 NA 12130 12237 11877 17377 NA 12219 17272 20384 NA NA
Danio rerio DrZebrafish 12722 4930 8038 4360 9388 4815 4515 6774 6862 NA NA
Gallus gallus GgChicken 18247 12694 13605 14162 3634 NA 12631 16377 23028 NA NA
Homo sapiens Hs133A 12582 12055 13093 10212 17573 11999 18554 42587 38914 NA NA
Homo sapiens Hs133Av2 12535 12055 13093 10212 17573 11999 18554 42587 38914 NA NA
Homo sapiens Hs133B 13058 6487 9978 8841 9109 6273 10376 21310 19601 NA NA
Homo sapiens Hs133P 24112 17469 19488 18027 26121 17601 27666 62626 61646 NA NA
Homo sapiens Hs133X 24037 17514 19575 17653 25719 17473 27397 60156 56618 NA NA
Homo sapiens Hs95Av2 7722 8322 8981 7084 12234 8183 12587 28070 25765 NA NA
Homo sapiens HsEx10stv2 NA NA NA 39843 34951 22460 45220 89638 405311 NA NA
Homo sapiens HsFocus 7975 7776 8471 6501 11132 7833 11895 25896 20700 NA NA
Mus musculus Mm11KsubA 2169 4255 5139 4250 6022 4450 5121 7353 8252 NA NA
Mus musculus Mm11KsubB 2532 3121 3531 2704 3969 2972 3518 5663 7742 NA NA
Mus musculus Mm430 20770 16105 18360 18162 26180 16578 20141 30764 35504 NA NA
Mus musculus Mm430A 13007 12114 13457 12024 17209 12453 14820 22768 25855 NA NA
Mus musculus Mm430B 12015 5726 9246 8742 11304 5923 7286 10322 11106 NA NA
Mus musculus Mm74Av1 8155 7157 8811 7087 9750 7258 8485 12460 14073 NA NA
Mus musculus Mm74Av2 8155 7953 8984 7586 10776 7941 9385 13809 15613 NA NA
Mus musculus MmEx10stv1 NA NA NA 34687 43029 23653 30557 51344 283623 NA NA
Oryza sativa OsRice 28334 NA 1174 NA 23600 NA NA NA NA 45047 NA
Pan troglodytes Hs133A NA NA NA NA NA 4703 10676 16413 16326 NA NA
Pan troglodytes Hs133Av2 NA NA NA NA NA 4703 10676 16413 16326 NA NA
Pan troglodytes Hs133B NA NA NA NA NA 2214 5092 7244 7158 NA NA
Pan troglodytes Hs133P NA NA NA NA NA 7333 15486 23772 24877 NA NA
Pan troglodytes Hs133X NA NA NA NA NA 6021 15039 22614 23315 NA NA
Pan troglodytes Hs95Av2 NA NA NA NA NA 2778 7238 10739 11055 NA NA
Pan troglodytes HsEx10stv2 NA NA NA NA NA 17572 22162 39532 167096 NA NA
Pan troglodytes HsFocus NA NA NA NA NA 2543 6738 9634 8517 NA NA
Rattus norvegicus Rn230 20675 8365 13279 14640 20302 10265 8704 11539 12447 NA NA
Rattus norvegicus Rn230A 12412 6280 9771 8956 14247 7733 6621 8705 8993 NA NA
Rattus norvegicus Rn230B 11087 2645 6022 6682 8234 3248 2538 3384 3635 NA NA
Rattus norvegicus Rn34A 5003 3848 4972 4215 6263 4040 3749 5304 7107 NA NA
Rattus norvegicus RnEx10stv1 NA NA NA 25447 41864 20342 21022 30620 183125 NA NA
Vitis vinifera VvGrape 10819 NA NA NA NA NA NA NA NA 11348 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
ENSG4 Canis familiaris CfCanine2 934 80 17207 24.4 85.4 7.4
ENSG4 Drosophila melanogaster DmDrosophila2 214 329 13058 67.4 99 4.1
ENSG4 Drosophila melanogaster DmGenome1 170 259 11960 92.3 98.8 3.7
ENSG4 Danio rerio DrZebrafish 1904 1489 3026 16.1 76.4 56.1
ENSG4 Gallus gallus GgChicken 1274 1211 11420 21.3 77.8 21.8
ENSG4 Homo sapiens Hs133A 774 7273 11281 42.1 91.2 42.8
ENSG4 Homo sapiens Hs133Av2 774 7273 11281 42.1 91.2 42.8
ENSG4 Homo sapiens Hs133B 583 4472 5904 50.7 91.1 46.9
ENSG4 Homo sapiens Hs133P 1111 11308 16358 39.1 90.3 44.2
ENSG4 Homo sapiens Hs133X 1250 11133 16264 49.7 90.5 44.3
ENSG4 Homo sapiens Hs95Av2 587 4852 7735 48.3 91.1 42.5
ENSG4 Homo sapiens HsFocus 480 4599 7296 50.2 93.5 41.7
ENSG4 Mus musculus Mm11KsubA 632 1498 3623 38.6 87 39.8
ENSG4 Mus musculus Mm11KsubB 580 977 2541 19.6 74.2 43.6
ENSG4 Mus musculus Mm430 1733 5769 14372 37.4 82.9 37.1
ENSG4 Mus musculus Mm430A 1274 3980 10840 39.1 86 35
ENSG4 Mus musculus Mm430B 1126 2686 4600 47.2 83.9 47.4
ENSG4 Mus musculus Mm74Av1 1100 2428 6057 41.7 85.7 39.6
ENSG4 Mus musculus Mm74Av2 1230 2662 6723 36.9 78.3 40.3
ENSG4 Rattus norvegicus Rn230 902 1241 7463 30.2 84.2 25.2
ENSG4 Rattus norvegicus Rn230A 555 896 5725 35 89.2 22.1
ENSG4 Rattus norvegicus Rn230B 560 453 2085 25.1 78.2 36.4
ENSG4 Rattus norvegicus Rn34A 354 255 3494 22.2 83.1 18.4
ENTREZG Canis familiaris CfCanine2 1333 283 15578 18.7 79.1 13
ENTREZG Danio rerio DrZebrafish 6576 1304 3511 14.3 71.5 72.4
ENTREZG Homo sapiens Hs133A 1717 368 11631 36.5 81.4 18.7
ENTREZG Homo sapiens Hs133Av2 1717 368 11631 36.5 81.4 18.7
ENTREZG Homo sapiens Hs133B 4583 390 5883 33.7 64.6 51.9
ENTREZG Homo sapiens Hs133P 3579 513 17088 24.2 59.9 29.5
ENTREZG Homo sapiens Hs133X 3794 537 16936 31.3 61.6 30.2
ENTREZG Homo sapiens Hs95Av2 1225 304 7879 43.6 83 20
ENTREZG Homo sapiens HsFocus 902 236 7597 48.6 91.9 14.2
ENTREZG Mus musculus Mm11KsubA 1305 368 4082 37.2 83.6 33.3
ENTREZG Mus musculus Mm11KsubB 871 270 2702 19.6 71.3 37.4
ENTREZG Mus musculus Mm430 5998 581 15997 26.5 63.6 36.9
ENTREZG Mus musculus Mm430A 1972 551 11902 35.3 79.5 21.3
ENTREZG Mus musculus Mm430B 7125 534 5389 34 63.5 64
ENTREZG Mus musculus Mm74Av1 2388 513 6745 36.4 75.3 35.3
ENTREZG Mus musculus Mm74Av2 1845 496 7445 34.9 73.5 29.4
ENTREZG Rattus norvegicus Rn230 3489 370 9895 25.9 64.7 36.3
ENTREZG Rattus norvegicus Rn230A 2452 321 7412 34.1 77.8 31.3
ENTREZG Rattus norvegicus Rn230B 2938 134 3114 25 62.9 55.7
ENTREZG Rattus norvegicus Rn34A 1192 199 3841 21.1 74.7 32.4
REFSEQ Arabidopsis thaliana AtGenome 1338 2649 5995 75.4 97 40.3
REFSEQ Arabidopsis thaliana AtH1 3750 6532 17933 91.3 99 36.6
REFSEQ Canis familiaris CfCanine2 16235 5 638 54.2 72.1 96.3
REFSEQ Drosophila melanogaster DmDrosophila2 3349 8651 10331 96.3 98.7 53.8
REFSEQ Drosophila melanogaster DmGenome1 3038 8178 9199 93.3 98.6 55.1
REFSEQ Danio rerio DrZebrafish 2282 3632 5756 36.8 77.8 55.5
REFSEQ Gallus gallus GgChicken 10052 81 3553 55.2 76.4 75
REFSEQ Homo sapiens Hs133A 4243 8723 8850 57.1 84.3 60.7
REFSEQ Homo sapiens Hs133Av2 4243 8723 8850 57.1 84.3 60.7
REFSEQ Homo sapiens Hs133B 5486 4617 4492 44.1 67.7 71.7
REFSEQ Homo sapiens Hs133P 6259 12892 13229 38 63.2 63.2
REFSEQ Homo sapiens Hs133X 6494 12638 13081 41.9 64.9 63.5
REFSEQ Homo sapiens Hs95Av2 3136 6389 5845 56.7 85.3 63.4
REFSEQ Homo sapiens HsFocus 2796 5457 5675 69.9 93.3 59.8
REFSEQ Mus musculus Mm11KsubA 1415 2299 3723 53.2 84.9 52.8
REFSEQ Mus musculus Mm11KsubB 984 1422 2547 41.3 75.2 53.5
REFSEQ Mus musculus Mm430 4464 12284 13896 42.1 67.2 58.4
REFSEQ Mus musculus Mm430A 2538 6290 10919 55.5 82.5 46.5
REFSEQ Mus musculus Mm430B 5396 7454 3850 43.7 66.2 79.1
REFSEQ Mus musculus Mm74Av1 2615 3554 6196 51.5 77.8 52.9
REFSEQ Mus musculus Mm74Av2 2145 3937 6839 48.4 75.9 50.3
REFSEQ Oryza sativa OsRice 240 22666 934 NA 7.5 99.2
REFSEQ Rattus norvegicus Rn230 2134 9157 11145 45.6 70.8 54.1
REFSEQ Rattus norvegicus Rn230A 1488 5964 8283 59.1 83.7 49.1
REFSEQ Rattus norvegicus Rn230B 2398 4610 3624 41.5 69.3 68.8
REFSEQ Rattus norvegicus Rn34A 746 2037 4226 52.8 82 43.1
UG Canis familiaris CfCanine2 6050 3124 6917 29.6 75 58.2
UG Danio rerio DrZebrafish 9304 942 3418 19.4 80.7 76.7
UG Gallus gallus GgChicken 8779 4694 9468 36.8 78.1 60.8
UG Homo sapiens Hs133A 3442 1072 9140 43.3 82.4 36
UG Homo sapiens Hs133Av2 3427 1104 9108 43.4 82.5 36.2
UG Homo sapiens Hs133B 6021 1804 7037 40.6 74 56.3
UG Homo sapiens Hs133P 8828 2743 15284 35.1 73.1 47.8
UG Homo sapiens Hs133X 9044 2660 14993 38.7 72.3 49
UG Homo sapiens Hs95Av2 2141 1503 5581 46 81.6 42.9
UG Homo sapiens HsFocus 2040 566 5935 53.5 91.3 32
UG Mus musculus Mm11KsubA 542 2623 1627 44 79.6 68.8
UG Mus musculus Mm11KsubB 565 737 1967 31 73.9 46
UG Mus musculus Mm430 4094 1486 16676 41.2 74.1 31.1
UG Mus musculus Mm430A 1743 760 11264 50.8 83.4 21.8
UG Mus musculus Mm430B 4357 1084 7658 43.4 73.9 46.4
UG Mus musculus Mm74Av1 2255 1187 5900 47 76.2 41.9
UG Mus musculus Mm74Av2 1637 1068 6518 46.6 78.6 34.4
UG Rattus norvegicus Rn230 7755 1720 12920 51.8 84.2 44.5
UG Rattus norvegicus Rn230A 4319 863 8093 57.7 87.7 40.7
UG Rattus norvegicus Rn230B 5309 904 5778 52.6 86.8 53.3
UG Rattus norvegicus Rn34A 1420 632 3583 42.4 78.1 41
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.
4. Include definition from CORE and VEGA. Some of the definition may be redundant.  

 


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