I realized that I totally forgot about the fact that there are mismatch probes on the HG-U133 Plus 2.0 arrays which explains why there are x2 the number of probes for each probeset. For those interested in just grabbing the pm probes, you can do something like this:
ps <- "1053_at" types <- "pm cells <- lapply(types, FUN=function(type) identifyCells(cdf, types=type)) names(cells) <- types pm_cells <- unlist(cells["pm"]) probe_cells <- getCellIndices(cdf, units=indexOf(cdf, names=ps), unlist=TRUE) probe_cells <- intersect(pm_cells, probe_cells) #retrieves only the PM probes This will return just the probe_cells of PM probes. And then you can use: m <- getIntensities(cs, indices=probe_cells) To get the intensities of just those probes. Fong On Dec 21, 11:36 am, Fong <fongchunc...@gmail.com> wrote: > Hi all, > > I've been looking at probe-level data for HG-U133 Plus 2.0 arrays and > following the tutorial listed at "http://groups.google.com/group/aroma- > affymetrix/web/data-affymetrixcelset-object". When I run the > readUnits(csOrig,unit=1) #gets the first unit (aka probeset), where > csOrig is a celSet for HG-U133 Plus 2.0 arrays, I am getting a higher > than expected number of probes grouped to this probeset. In this > case, unit=1 is the probeset "AFFX-BioB-5_at", and it reports as > having 40 probes: > > Here is the output: > > readUnits(cs, unit=1) > $`AFFX-BioB-5_at` > $`AFFX-BioB-5_at`$`AFFX-BioB-5_at` > $`AFFX-BioB-5_at`$`AFFX-BioB-5_at`$intensities > [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [, > 13] > [1,] 391 286 384 477 407 405 328 506 402 344 344 348 > 377 > [2,] 89 81 92 119 116 103 92 99 113 100 84 > 89 96 > [3,] 198 171 254 256 233 209 181 259 248 214 164 153 > 223 > [4,] 68 87 86 97 89 84 78 63 89 79 80 > 68 81 > [5,] 647 634 698 727 698 656 600 905 701 731 656 733 > 805 > [6,] 166 172 177 220 205 163 190 228 214 221 229 179 > 175 > [7,] 148 117 144 200 153 112 107 165 155 152 137 124 > 164 > [8,] 105 86 86 93 84 74 77 80 78 86 88 > 85 60 > [9,] 507 511 561 619 520 499 532 715 661 621 539 596 > 600 > [10,] 487 247 316 380 344 400 268 374 449 393 364 278 > 375 > [11,] 650 559 688 672 690 619 665 836 793 679 679 729 > 793 > [12,] 203 161 260 229 233 194 201 269 260 234 189 222 > 225 > [13,] 1046 862 1174 1175 1054 998 974 1318 1145 1057 1119 1150 > 1356 > [14,] 502 436 566 566 509 501 432 603 522 514 507 510 > 583 > [15,] 1022 863 1152 1167 1143 1021 963 1308 1145 1152 1166 1134 > 1399 > [16,] 302 218 301 355 346 268 249 386 317 326 275 272 > 398 > [17,] 894 744 1020 1070 858 858 794 1181 959 991 870 1025 > 1166 > [18,] 243 208 303 289 261 257 255 259 273 290 221 228 > 313 > [19,] 382 337 470 381 369 373 383 520 455 384 415 425 > 447 > [20,] 104 109 113 147 140 120 119 127 128 136 129 96 > 110 > [21,] 462 332 427 428 389 411 343 545 539 449 419 463 > 504 > [22,] 156 145 137 169 141 166 147 146 164 171 169 134 > 129 > [23,] 238 148 246 252 249 215 190 281 209 198 191 203 > 201 > [24,] 89 93 80 106 122 89 90 85 89 93 92 > 87 88 > [25,] 240 201 331 246 230 249 180 277 252 250 265 222 > 286 > [26,] 109 96 103 147 109 117 89 88 95 113 113 > 77 85 > [27,] 160 163 176 178 163 205 158 170 180 163 162 168 > 204 > [28,] 97 91 102 155 116 142 104 101 97 104 102 > 80 90 > [29,] 614 532 623 628 576 564 550 701 575 623 570 485 > 689 > [30,] 114 82 99 93 118 109 94 105 114 90 91 > 86 97 > [31,] 179 168 147 165 200 169 133 173 169 146 145 148 > 140 > [32,] 614 458 459 612 846 551 497 800 805 611 508 383 > 454 > [33,] 305 330 346 339 300 297 322 375 383 394 355 326 > 369 > [34,] 116 127 127 146 170 131 137 140 139 129 141 122 > 124 > [35,] 145 127 167 164 174 148 167 160 188 190 153 151 > 170 > [36,] 114 80 100 128 148 102 121 97 105 135 100 > 89 89 > [37,] 175 154 227 184 157 144 123 185 164 161 156 167 > 162 > [38,] 71 73 70 84 93 91 105 77 92 78 77 > 62 81 > [39,] 802 498 744 807 888 692 617 798 743 720 720 778 > 881 > [40,] 274 213 311 310 320 258 250 321 278 283 291 199 > 254 > > I've looked around in the annotation files from affymetrix and there > are only 20 probes for this probeset. Other probesets I've looked at > have this issue too. It seems that the number of probes groupt to > that probeset are always doubled. I am using the cdf which is located > athttp://aroma-project.org/node/26, and the "Binary version of the > CDF file (shown above) from Affymetrix. 54,675 units." > > Is this a mistake in the cdf file grouping of probes to probesets, or > am I misunderstanding what the readUnits/readIntensities functions are > doing? > > Fong -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
