Correct. FYI, it is more straightforward to do: > library("aroma.affymetrix"); > cdf <- AffymetrixCdfFile$byChipType("HG-U133_Plus_2"); > units <- indexOf(cdf, names="1053_at"); > print(units); [1] 64 > cells <- getCellIndices(cdf, units=units, stratifyBy="pm"); > print(cells);
$`1053_at` $`1053_at`$groups $`1053_at`$groups$`1053_at` $`1053_at`$groups$`1053_at`$indices [1] 1193929 48229 1014367 1076821 975016 201506 895292 [8] 1170808 81075 134485 714108 956498 429738 62512 [15] 462278 276396 Compare with: > cells <- getCellIndices(cdf, units=units, stratifyBy="pmmm"); > print(cells); $`1053_at` $`1053_at`$groups $`1053_at`$groups$`1053_at` $`1053_at`$groups$`1053_at`$indices [,1] [,2] [,3] [,4] [,5] [,6] [,7] pm 1193929 48229 1014367 1076821 975016 201506 895292 mm 1195093 49393 1015531 1077985 976180 202670 896456 [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] pm 1170808 81075 134485 714108 956498 429738 62512 462278 mm 1171972 82239 135649 715272 957662 430902 63676 463442 [,16] pm 276396 mm 277560 and > cells <- getCellIndices(cdf, units=units); > print(cells); $`1053_at` $`1053_at`$groups $`1053_at`$groups$`1053_at` $`1053_at`$groups$`1053_at`$indices [1] 1193929 1195093 48229 49393 1014367 1015531 1076821 [8] 1077985 975016 976180 201506 202670 895292 896456 [15] 1170808 1171972 81075 82239 134485 135649 714108 [22] 715272 956498 957662 429738 430902 62512 63676 [29] 462278 463442 276396 277560 /Henrik On Wed, Dec 22, 2010 at 7:54 PM, Fong <fongchunc...@gmail.com> wrote: > 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/ > -- 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/