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.
>
>
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--
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.
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