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