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Statistics of Affymetrix and Custom CDF Files (Version 2)
Table 1. Target Count for Affymetrix and Custom Probe Sets
Species | Chiptype | Affy-UG1 | Affy-ENSG2 | Affy-Refseq3 | UG | DoTS | Refseq | EntrezG | ENSG3 | ENST3 | ENSE3 | Affy-SNP | UG-SNP |
Hs | Hs133A | 12755 | 11569 | 12037 | 12764 | 101619 | 15639 | 2825 | 11394 | 16885 | 18091 | 22169 | 12610 |
Hs | Hs133Av2 | N/A | N/A | N/A | 12764 | 101619 | 15639 | 2825 | 11394 | 16885 | 18091 | 22169 | 12610 |
Hs | Hs133B | 12876 | 7129 | 7539 | 9051 | 56590 | 6838 | 1682 | 5285 | 7218 | 7603 | 22562 | 8999 |
Hs | Hs133P | 24410 | 15445 | 16389 | 21276 | 163556 | 22153 | 4616 | 16308 | 23961 | 27325 | 54540 | 21088 |
Hs | Hs133X | 13507 | 15442 | 16371 | 21065 | 153882 | 21941 | 4497 | 15999 | 22896 | 24694 | 60993 | 20893 |
Hs | Hs95Av2 | 7835 | 8073 | 8374 | 8748 | 67911 | 10797 | 1919 | 7615 | 11029 | 11995 | 12537 | 8675 |
Hs | HsFocus | N/A | N/A | N/A | 7996 | 55623 | 10359 | 1747 | 7438 | 10471 | 9793 | 8727 | 7903 |
Mm | Mm430 | 24388 | 13313 | 14448 | 23411 | 95998 | 16623 | 15271 | 14820 | 11602 | 22860 | N/A | N/A |
Mm | Mm430A | 12961 | 11160 | 11891 | 13280 | 66391 | 12527 | 11479 | 11090 | 8750 | 17069 | N/A | N/A |
Mm | Mm430B | 14224 | 4936 | 5479 | 12373 | 32871 | 5002 | 4660 | 4761 | 3500 | 6506 | N/A | N/A |
Mm | Mm74Av2 | 7685 | 7515 | 8004 | 8635 | 39895 | 7721 | 7111 | 6898 | 5261 | 10196 | N/A | N/A |
Pt | Hs133A | N/A | N/A | N/A | 11366 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133Av2 | N/A | N/A | N/A | 11367 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133B | N/A | N/A | N/A | 8401 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133P | N/A | N/A | N/A | 19245 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133X | N/A | N/A | N/A | 19037 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs95Av2 | N/A | N/A | N/A | 7816 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | HsFocus | N/A | N/A | N/A | 7111 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Rn | Rn230 | 20428 | 4039 | 4670 | 18172 | N/A | 9200 | 8644 | 7064 | 8759 | 9191 | N/A | N/A |
Rn | Rn230A | 12030 | 3960 | 4503 | 10756 | N/A | 7058 | 6591 | 5280 | 6544 | 6620 | N/A | N/A |
Rn | Rn230B | 10372 | 584 | 742 | 8554 | N/A | 2536 | 2396 | 2015 | 2475 | 2629 | N/A | N/A |
Rn | Rn34A | 4857 | 2970 | 3312 | 5387 | N/A | 4082 | 3764 | 3263 | 4269 | 6193 | N/A | N/A |
1. Affy-UG is the count of unique UniGene ID that each Affymetrix
GeneChip can represent. It is derived by mapping the "Representative
Public ID" provided by Affymetrix to the Latest UniGene Build at the
time of building our custom CDF files. 2. Affy-ENSG and Affy-Refseq counts are based on the latest version of Affymetrix GeneChip annotation files from www.affymetrix.com 3. To be consistent with Affymetrix annotation, only target numbers derived from the CORE division of ENSEMBL are listed here. Please refer to Table 5 for the distribution of custom probe sets across different ENSEMBL divisions. |
Table 2. Affymetrix UG Probe Sets vs. Custom UG Probe Sets
Species | Chiptype | UGID Shared | Affy Only UGID | Custom Only UGID | Identical Probe Sets1 | Difference <= 3 Probes2 | Difference >= 50%3 |
Hs | Hs133A | 11313 | 1442 | 1451 | 4951 | 7750 | 2327 |
Hs | Hs133Av2 | N/A | N/A | 12764 | N/A | N/A | N/A |
Hs | Hs133B | 7818 | 5058 | 1233 | 3357 | 4960 | 2041 |
Hs | Hs133P | 18824 | 5586 | 2452 | 6485 | 10177 | 5751 |
Hs | Hs133X | 8159 | 5348 | 12906 | 2311 | 3174 | 4386 |
Hs | Hs95Av2 | 6877 | 958 | 1871 | 3366 | 4706 | 1423 |
Hs | HsFocus | N/A | N/A | 7996 | N/A | N/A | N/A |
Mm | Mm430 | 19988 | 4400 | 3423 | 7229 | 12026 | 5031 |
Mm | Mm430A | 11395 | 1566 | 1885 | 4756 | 7640 | 2500 |
Mm | Mm430B | 10374 | 3850 | 1999 | 4008 | 6739 | 2196 |
Mm | Mm74Av2 | 6321 | 1364 | 2314 | 2677 | 4036 | 1525 |
Pt | Hs133A | N/A | N/A | 11366 | N/A | N/A | N/A |
Pt | Hs133Av2 | N/A | N/A | 11367 | N/A | N/A | N/A |
Pt | Hs133B | N/A | N/A | 8401 | N/A | N/A | N/A |
Pt | Hs133P | N/A | N/A | 19245 | N/A | N/A | N/A |
Pt | Hs133X | N/A | N/A | 19037 | N/A | N/A | N/A |
Pt | Hs95Av2 | N/A | N/A | 7816 | N/A | N/A | N/A |
Pt | HsFocus | N/A | N/A | 7111 | N/A | N/A | N/A |
Rn | Rn230 | 16208 | 4220 | 1964 | 6143 | 10896 | 3351 |
Rn | Rn230A | 9618 | 2412 | 1138 | 4037 | 7062 | 1659 |
Rn | Rn230B | 7567 | 2805 | 987 | 2964 | 5295 | 1348 |
Rn | Rn34A | 4055 | 802 | 1332 | 1230 | 2140 | 1326 |
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. |
Table 3. Affymetrix UG Probe Sets vs. Custom UG-SNP Probe Sets
Species | Chiptype | UGID Shared | Affy Only UGID | Custom Only UGID | Identical Probe Sets1 | Difference <= 3 Probes2 | Difference >= 50%3 |
Hs | Hs133A | 11188 | 1567 | 1576 | 2889 | 7251 | 2323 |
Hs | Hs133Av2 | N/A | N/A | 12764 | N/A | N/A | N/A |
Hs | Hs133B | 7781 | 5095 | 1270 | 2332 | 4779 | 2051 |
Hs | Hs133P | 18667 | 5743 | 2609 | 4013 | 9531 | 5763 |
Hs | Hs133X | 8116 | 5391 | 12949 | 1663 | 3066 | 4346 |
Hs | Hs95Av2 | 6833 | 1002 | 1915 | 2127 | 4238 | 1476 |
Hs | HsFocus | N/A | N/A | 7996 | N/A | N/A | N/A |
Pt | Hs133A | N/A | N/A | 11366 | N/A | N/A | N/A |
Pt | Hs133Av2 | N/A | N/A | 11367 | N/A | N/A | N/A |
Pt | Hs133B | N/A | N/A | 8401 | N/A | N/A | N/A |
Pt | Hs133P | N/A | N/A | 19245 | N/A | N/A | N/A |
Pt | Hs133X | N/A | N/A | 19037 | N/A | N/A | N/A |
Pt | Hs95Av2 | N/A | N/A | 7816 | N/A | N/A | N/A |
Pt | HsFocus | N/A | N/A | 7111 | N/A | N/A | N/A |
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. |
Table 4. Affymetrix ENSG Probe Sets vs. Custom ENSG Probe Sets
Species | Chiptype | ENSG Shared | Affy Only ENSG | Custom Only ENSG | Identical Probe Sets1 | Difference <= 3 Probes2 | Difference >= 50%3 |
Hs | Hs133A | 10566 | 1003 | 828 | 3600 | 7079 | 1694 |
Hs | Hs133Av2 | N/A | N/A | 11394 | N/A | N/A | N/A |
Hs | Hs133B | 4414 | 2715 | 871 | 1523 | 2559 | 1279 |
Hs | Hs133P | 14371 | 1074 | 1937 | 3532 | 6938 | 4567 |
Hs | Hs133X | 14187 | 1255 | 1812 | 4536 | 7083 | 4565 |
Hs | Hs95Av2 | 7124 | 949 | 491 | 2878 | 4649 | 1139 |
Hs | HsFocus | N/A | N/A | 7438 | N/A | N/A | N/A |
Mm | Mm430 | 10761 | 2552 | 4059 | 2506 | 5491 | 3035 |
Mm | Mm430A | 9075 | 2085 | 2015 | 2530 | 5636 | 1727 |
Mm | Mm430B | 2452 | 2484 | 2309 | 726 | 1303 | 725 |
Mm | Mm74Av2 | 5675 | 1840 | 1223 | 1671 | 3041 | 1310 |
Rn | Rn230 | 2985 | 1054 | 4079 | 471 | 1462 | 1155 |
Rn | Rn230A | 2911 | 1049 | 2369 | 510 | 1591 | 948 |
Rn | Rn230B | 102 | 482 | 1913 | 12 | 45 | 38 |
Rn | Rn34A | 2250 | 720 | 1013 | 267 | 796 | 811 |
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. |
Table 5. Affymetrix Refseq Probe Sets vs. Custom Refseq Probe Sets
Species | Chiptype | Refseq Shared | Affy Only Refseq | Custom Only Refseq | Identical Probe sets1 | Differnece <= 3 Probes2 | Differnece >= 50%3 |
Hs | Hs133A | 8984 | 3053 | 6655 | 3186 | 6364 | 1386 |
Hs | Hs133Av2 | N/A | N/A | 15639 | N/A | N/A | N/A |
Hs | Hs133B | 3898 | 3641 | 2940 | 1273 | 2281 | 1141 |
Hs | Hs133P | 12799 | 3590 | 9354 | 3270 | 6538 | 4141 |
Hs | Hs133X | 12711 | 3660 | 9230 | 4175 | 6559 | 4143 |
Hs | Hs95Av2 | 5913 | 2461 | 4884 | 2236 | 3912 | 917 |
Hs | HsFocus | N/A | N/A | 10359 | N/A | N/A | N/A |
Mm | Mm430 | 12418 | 2030 | 4205 | 2677 | 6223 | 3836 |
Mm | Mm430A | 10303 | 1588 | 2224 | 2615 | 6272 | 2188 |
Mm | Mm430B | 2752 | 2727 | 2250 | 757 | 1466 | 833 |
Mm | Mm74Av2 | 6391 | 1613 | 1330 | 1579 | 3298 | 1608 |
Rn | Rn230 | 4086 | 584 | 5114 | 837 | 2446 | 1158 |
Rn | Rn230A | 3941 | 562 | 3117 | 912 | 2631 | 846 |
Rn | Rn230B | 230 | 512 | 2306 | 42 | 126 | 65 |
Rn | Rn34A | 2918 | 394 | 1164 | 481 | 1349 | 654 |
Table 6. Distribution of ENSEMBL Probe Sets in ENSEMBL CORE, ESTGENE and VEGA Databases
Species | Chiptype | ENSEMBL Division | ENSG | ENST | ENSE |
Hs | Hs133A | CORE | 11394 | 16885 | 18091 |
Hs | Hs133A | EST | 5997 | 10339 | 9407 |
Hs | Hs133A | VEGA | 3174 | 4842 | 5188 |
Hs | Hs133Av2 | CORE | 11394 | 16885 | 18091 |
Hs | Hs133Av2 | EST | 5997 | 10339 | 9407 |
Hs | Hs133Av2 | VEGA | 3174 | 4842 | 5188 |
Hs | Hs133B | CORE | 5285 | 7218 | 7603 |
Hs | Hs133B | EST | 2956 | 4721 | 4492 |
Hs | Hs133B | VEGA | 1601 | 2490 | 2606 |
Hs | Hs133P | CORE | 16308 | 23961 | 27325 |
Hs | Hs133P | EST | 9363 | 15787 | 15002 |
Hs | Hs133P | VEGA | 4472 | 7034 | 8039 |
Hs | Hs133X | CORE | 15999 | 22896 | 24694 |
Hs | Hs133X | EST | 8195 | 13458 | 12625 |
Hs | Hs133X | VEGA | 4422 | 6827 | 7327 |
Hs | Hs95Av2 | CORE | 7615 | 11029 | 11995 |
Hs | Hs95Av2 | EST | 3505 | 5863 | 6094 |
Hs | Hs95Av2 | VEGA | 2201 | 3211 | 3489 |
Hs | HsFocus | CORE | 7438 | 10471 | 9793 |
Hs | HsFocus | EST | 3292 | 5435 | 4486 |
Hs | HsFocus | VEGA | 2052 | 2954 | 2743 |
Mm | Mm430 | CORE | 14820 | 11602 | 22860 |
Mm | Mm430 | EST | 8722 | 15232 | 13478 |
Mm | Mm430A | CORE | 11090 | 8750 | 17069 |
Mm | Mm430A | EST | 6423 | 11317 | 9812 |
Mm | Mm430B | CORE | 4761 | 3500 | 6506 |
Mm | Mm430B | EST | 2541 | 4231 | 3783 |
Mm | Mm74Av2 | CORE | 6898 | 5261 | 10196 |
Mm | Mm74Av2 | EST | 3549 | 6048 | 5801 |
Rn | Rn230 | CORE | 7064 | 8759 | 9191 |
Rn | Rn230 | EST | 7574 | 12316 | 11585 |
Rn | Rn230A | CORE | 5280 | 6544 | 6620 |
Rn | Rn230A | EST | 5077 | 8761 | 7669 |
Rn | Rn230B | CORE | 2015 | 2475 | 2629 |
Rn | Rn230B | EST | 2775 | 3911 | 4065 |
Rn | Rn34A | CORE | 3263 | 4269 | 6193 |
Rn | Rn34A | EST | 2506 | 4446 | 5017 |
Table 7. Probe Utilization in Affymetrix and Custom CDF files
Species | Chiptype | Affy Total | Affy-UG | Affy-ENSG | Affy-Refseq | UG | DoTS | Refseq | EntrezG | ENSG4 | ENST4 | ENSE4 | Affy-SNP | UG-SNP |
Hs | Hs133A | 246799 | 220314 | 214160 | 219510 | 179140 | 198428 | 162349 | 32764 | 157823(163386) | 158139(163673) | 146278(151897) | 230603 | 170000 |
Hs | Hs133Av2 | 246799 | N/A | N/A | N/A | 179140 | 198428 | 162349 | 32764 | 157823(163386) | 158139(163673) | 146278(151897) | 230603 | 170004 |
Hs | Hs133B | 248336 | 214911 | 126789 | 132762 | 116568 | 208766 | 68638 | 15912 | 71553(77340) | 71746(77493) | 67184(72975) | 236685 | 112149 |
Hs | Hs133P | 603158 | 532303 | 384769 | 398831 | 345629 | 495100 | 257886 | 55376 | 254105(267012) | 254683(267511) | 236739(249717) | 570872 | 330495 |
Hs | Hs133X | 672804 | 258949 | 414526 | 430152 | 374076 | 546684 | 277443 | 62371 | 272868(287728) | 273008(287771) | 266867(281758) | 634588 | 356377 |
Hs | Hs95Av2 | 197695 | 160615 | 175177 | 179005 | 146919 | 163103 | 134208 | 27511 | 130609(135424) | 130904(135710) | 126668(131499) | 185369 | 139389 |
Hs | HsFocus | 97349 | N/A | N/A | N/A | 78447 | 81660 | 76395 | 15442 | 74039(75561) | 74130(75637) | 67869(69405) | 90518 | 73888 |
Mm | Mm430 | 495374 | 421072 | 290291 | 306789 | 317351 | 343740 | 201813 | 199246 | 200168(210152) | 125950(166805) | 185567(195126) | N/A | N/A |
Mm | Mm430A | 248864 | 222386 | 210000 | 219029 | 182343 | 187750 | 149651 | 148062 | 147230(150908) | 93321(120884) | 135725(139333) | N/A | N/A |
Mm | Mm430B | 247610 | 199720 | 81398 | 88964 | 136255 | 156554 | 52666 | 51746 | 53428(59731) | 33005(46361) | 50250(56200) | N/A | N/A |
Mm | Mm74Av2 | 196670 | 143242 | 159110 | 166911 | 124586 | 128653 | 103023 | 102172 | 100276(103372) | 63250(82762) | 96713(99755) | N/A | N/A |
Pt | Hs133A | 191015 | N/A | N/A | N/A | 136073 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133Av2 | 191015 | N/A | N/A | N/A | 136076 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133B | 194181 | N/A | N/A | N/A | 90447 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133P | 465845 | N/A | N/A | N/A | 264409 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs133X | 514390 | N/A | N/A | N/A | 284981 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | Hs95Av2 | 155376 | N/A | N/A | N/A | 113050 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Pt | HsFocus | 75612 | N/A | N/A | N/A | 59265 | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Rn | Rn230 | 341459 | 288915 | 67478 | 75816 | 195421 | N/A | 88402 | 84620 | 58725(95913) | 59924(97411) | 48076(84976) | N/A | N/A |
Rn | Rn230A | 174526 | 158763 | 59569 | 65542 | 111640 | N/A | 65580 | 63013 | 43554(65849) | 44425(66833) | 35560(57841) | N/A | N/A |
Rn | Rn230B | 168033 | 131131 | 8210 | 10630 | 84520 | N/A | 23047 | 21822 | 15246(30414) | 15584(30943) | 12639(27478) | N/A | N/A |
Rn | Rn34A | 139137 | 107491 | 79676 | 86235 | 90150 | N/A | 66975 | 64317 | 50478(62280) | 51317(63199) | 46821(58641) | N/A | N/A |
* Value before the parenthesis is the probe count for the CORE division of ENSEMBL while value in parenthesis is the total count across all ENSEMBL divisions. |
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