[BioC] Affy RNA digestion plots
Matt Wayland
mwayland at hgmp.mrc.ac.uk
Mon Mar 10 00:07:16 MET 2003
Dear All,
I am using the AffyRNAdeg feature in the Affy package to do some QC on
Affymetrix U133A chips. I have found the RNA digestion plots useful, but have
been disappointed that no scale is provided on the ordinate axis (mean
intensity). To try to get round this problem I printed the means.by.number
data (see below) and plotted these values against position in probeset using
MS Excel. I was surprised to find that the graphs produced in MS Excel had
quite different profiles to those displayed in the RNA digestion plots. I had
assumed that the RNA digestion plots were simply the mean signal intensity vs
position in probeset, but this doesn't appear to be the case. I would be very
grateful for some clarification on what data are used to generate the RNA
digestion plots.
Many thanks,
Matt Wayland
> data <- ReadAffy()
> AffyRNAdeg(data)
$N
[1] 21748
$sample.names
[1] "mr270_u133a_031002.cel" "mr273_u133a_041002.cel"
"mr274_u133a_041002.cel"
[4] "mr275_u133a_031002.cel" "mr276_u133a_031002.cel"
"mr279_u133a_031002.cel"
[7] "mr283_u133a_041002.cel" "mr289_u133a_041002.cel"
"mr290_u133a_041002.cel"
[10] "mr304_u133a_031002.cel" "mr387_u133a_141102.cel"
"mr388_u133a_141102.cel"
[13] "mr389_u133a_141102.cel" "mr390_u133a_141102.cel"
"mr391_u133a_291102.cel"
[16] "mr392_u133a_141102.cel" "mr393_u133a_141102.cel"
"mr394_u133a_141102.cel"
[19] "mr394rescan_u133a_141102.cel" "mr395_u133a_141102.cel"
$means.by.number
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[,8] [,9] [,10]
[1,] 312.24324 319.41340 330.19704 336.34291 346.4428 352.20669 362.56459
369.15780 385.1667 401.8260
[2,] 314.26197 326.08707 341.49786 353.68829 364.3879 372.95726 388.60827
400.19313 418.4312 442.1922
[3,] 200.29662 207.87890 216.77583 225.35399 233.8228 241.10621 251.93380
260.68953 277.5727 300.0786
[4,] 265.58481 274.41516 285.67500 295.57530 301.0484 305.85731 316.23678
321.94475 336.1416 353.7683
[5,] 237.39643 249.04961 261.28215 272.73540 283.8943 294.63220 312.51102
327.19376 353.6499 382.2028
[6,] 331.94818 353.24510 368.40463 384.21897 399.4587 408.84340 430.72119
446.98323 476.0305 514.7243
[7,] 287.27735 300.31111 317.86892 331.14931 345.3910 355.08406 372.07448
388.42676 411.0557 438.4923
[8,] 237.09106 245.06492 259.27626 271.80332 283.0637 292.58623 307.96840
319.45045 340.4156 365.7162
[9,] 186.08333 195.41691 204.92691 212.64382 222.1514 229.31276 239.94625
251.62243 265.6125 286.7258
[10,] 230.73947 239.28730 251.03565 260.01666 268.1781 272.88936 284.42916
292.16157 306.4707 324.4112
[11,] 136.08890 143.72108 153.00208 157.94266 165.8060 171.14296 180.27605
188.01310 204.5086 217.9039
[12,] 75.63805 75.24983 80.96209 83.92029 86.2474 88.45327 91.94578
94.70696 100.5653 108.4616
[13,] 160.98618 158.10125 169.44953 172.39056 182.1134 188.22345 196.14362
203.95820 218.6914 236.5902
[14,] 107.41897 109.79777 118.57822 117.79826 127.4231 131.58506 138.51518
146.40628 160.8142 177.1633
[15,] 323.35902 328.81570 346.50632 353.27325 367.2940 377.31874 390.22261
402.47949 424.7832 446.2216
[16,] 167.15414 168.53799 179.82503 181.18348 187.9804 190.09142 196.09917
199.86315 210.4262 219.9084
[17,] 159.28877 166.78256 177.71656 183.49601 192.0320 197.17635 208.36922
215.73980 228.4682 241.3190
[18,] 198.81566 203.76260 217.75332 225.04835 230.2787 233.40515 245.21989
253.57868 267.9055 286.4034
[19,] 148.65748 152.64352 162.97836 168.89231 173.5515 177.82458 186.68972
193.92629 206.0257 222.0941
[20,] 183.36636 185.25957 202.40772 205.14033 213.6603 222.57077 233.51481
241.57686 260.0722 274.7090
[,11]
[1,] 410.9676
[2,] 455.7815
[3,] 317.0094
[4,] 359.2622
[5,] 406.5269
[6,] 540.2176
[7,] 458.6396
[8,] 384.3845
[9,] 302.4575
[10,] 331.7975
[11,] 231.5498
[12,] 117.5673
[13,] 259.4498
[14,] 201.1130
[15,] 465.6808
[16,] 229.0117
[17,] 249.2864
[18,] 303.8286
[19,] 235.6483
[20,] 291.9949
$ses
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[,9] [,10]
[1,] 2.979068 3.231999 3.248349 3.250654 3.447194 3.476177 3.716082 3.757014
4.133177 4.411707
[2,] 3.829038 3.928718 4.102715 4.609745 4.516899 4.388837 4.751339 4.993989
5.208078 5.501841
[3,] 2.272700 2.409056 2.561558 2.841119 2.966126 3.353292 3.178980 3.222258
3.619070 3.937812
[4,] 3.234827 3.272941 3.507344 3.884075 3.810236 3.684243 3.906516 4.058972
4.367417 5.073097
[5,] 2.953482 3.139142 3.412897 3.442658 3.806649 3.775800 4.154000 4.423420
5.304306 5.320836
[6,] 4.197838 5.371407 4.796802 5.010445 5.296268 5.207516 5.577430 5.829057
6.296543 6.822710
[7,] 3.475498 3.652136 4.027193 4.178229 4.437116 4.453714 4.670320 4.987660
5.412965 5.730075
[8,] 2.683317 2.738826 2.960752 3.323439 3.407421 3.462054 3.744526 3.877138
4.258952 4.598133
[9,] 2.311373 2.460344 2.620369 2.677764 2.974538 2.900155 3.108412 3.968042
3.601589 3.944426
[10,] 2.916247 2.978695 3.195304 3.311031 3.553794 3.425443 3.616121 3.768021
4.027213 4.341722
[11,] 2.931571 3.186962 3.284025 3.333178 3.245712 2.828830 3.081501 3.126273
4.067688 3.730686
[12,] 2.604686 1.479444 1.679853 2.606219 1.871085 1.608409 1.782902 1.764316
1.902870 2.161340
[13,] 3.976159 2.680064 2.794041 2.717706 3.049992 3.008136 3.218159 3.420893
3.589378 3.837071
[14,] 1.758184 1.935993 2.644799 1.696589 2.766873 2.038273 2.320435 2.294649
2.702354 2.948170
[15,] 3.721190 3.604611 3.789913 3.840027 4.134421 4.171883 4.488898 4.568958
4.995486 5.245748
[16,] 2.629582 2.613296 2.706862 2.698391 2.933360 2.768549 2.928804 2.940941
3.142305 3.304945
[17,] 2.510858 2.564136 2.744861 2.733718 3.072721 2.921840 3.186635 3.295633
3.553450 3.783224
[18,] 2.754253 2.807787 3.002772 3.702209 3.216456 3.087679 3.350453 3.465458
3.695412 3.998094
[19,] 2.228747 2.259477 2.381427 3.192412 2.629340 2.505280 2.675800 2.804494
3.001332 3.244188
[20,] 3.009231 2.884623 3.724703 3.099992 3.290124 3.285948 3.621516 3.657245
3.999635 4.170622
[,11]
[1,] 4.777215
[2,] 5.832783
[3,] 4.316643
[4,] 4.893812
[5,] 5.784268
[6,] 7.191177
[7,] 6.036151
[8,] 4.956178
[9,] 4.278462
[10,] 4.415401
[11,] 4.093272
[12,] 2.432913
[13,] 4.489310
[14,] 3.702477
[15,] 5.800004
[16,] 3.618422
[17,] 4.011745
[18,] 4.371609
[19,] 3.572301
[20,] 4.652216
$slope
[1] 2.101064 2.402095 2.668191 1.833786 2.826386 2.777475 2.760560 2.965249
2.599598 2.234974 2.318620
[12] 1.786323 2.296870 2.643422 2.511186 1.719133 2.243327 2.357818 2.444547
2.421390
$pvalue
[1] 8.527845e-11 2.473064e-11 2.025689e-11 8.520418e-10 2.637609e-11
1.827358e-11 1.978582e-11
[8] 7.230978e-12 3.092073e-09 7.012118e-11 1.688104e-10 9.052897e-10
5.886145e-09 4.604710e-10
[15] 1.504965e-11 8.610847e-10 3.944235e-10 6.846252e-11 3.396346e-11
1.641240e-11
> deg <- AffyRNAdeg(data)
> plotAffyRNAdeg(deg)
Dr Matt Wayland
Microarray Group
MRC HGMP-Resource Centre
Wellcome Trust Genome Campus
Hinxton
CB10 1SB
http://www.hgmp.mrc.ac.uk/Research/Microarray/index.jsp
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