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Sample GSM91925 Query DataSets for GSM91925
Status Public on Jan 12, 2006
Title MDA2AvsXY
Sample type genomic
 
Channel 1
Source name XY genomic DNA
Organism Homo sapiens
Characteristics XY genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name MDA2A genomic DNA
Organism Homo sapiens
Characteristics MDA2A genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35079.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 11, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3355
Series (2)
GSE4017 DNA copy number changes in prostate cancer cell lines
GSE4396 Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE UNF_VALUE
1 795 561 417 358 378 203 798 574 748 423 381 216 0 0 227 195 3524 470 0 6 0 0 581 597 1.862 .537 .567 .632 .735 3.592 32 170 .74 .55 60 2320 9030 44 50 41 47 0 578 369 209 .554 592 223 1.806 .584 -.853 -.775 -.775
2 953 824 434 376 519 448 898 697 512 437 464 321 0 0 365 485 530 425 46 40 5 11 967 785 1.158 .863 .692 .669 .773 2.811 52 266 1.056 .75 80 2460 9030 43 51 54 62 0 849 388 462 .89 719 331 1.124 .713 -.168 -.488 -.488
3 786 516 426 365 360 151 574 381 503 425 148 16 0 0 483 593 523 410 25 5 9 3 511 164 2.384 .419 .108 .5 .39 4.682 52 286 1.135 .57 80 2610 9030 43 51 69 77 -50 532 376 156 .432 393 16 2.313 .111 -1.21 -3.166
4 1307 887 387 351 920 536 1465 810 404 375 1078 459 0 0 420 230 142 153 100 100 91 83 1456 1537 1.716 .583 .426 .616 .658 2.071 12 104 .535 .79 50 2750 9030 44 49 84 89 0 914 362 553 .601 835 473 1.665 .439 -.735 -1.188 -1.188
5 1252 1099 392 373 860 726 1273 1060 409 385 881 687 0 0 333 342 123 142 100 100 100 96 1586 1568 1.185 .844 .78 .82 .869 1.5 32 176 .982 .76 60 2900 9030 44 50 99 105 0 1133 385 748 .87 1093 708 1.149 .804 -.2 -.315 -.315
6 1426 1228 363 336 1063 892 1431 1123 413 348 1068 787 0 0 495 440 238 120 100 100 93 96 1955 1855 1.192 .839 .737 .806 .782 1.543 32 216 .865 .85 70 3040 9020 42 49 112 119 0 1266 346 920 .865 1158 811 1.156 .76 -.209 -.397 -.397
7 1219 885 372 342 847 543 1268 932 397 355 896 590 0 0 432 271 145 123 96 93 90 84 1390 1486 1.56 .641 .658 .639 .703 1.897 32 176 .561 .78 60 3180 9030 44 50 127 133 0 912 353 560 .661 961 608 1.513 .679 -.597 -.559 -.559
8 1291 1169 400 403 891 766 1313 1090 633 667 913 687 0 0 444 457 940 1108 46 21 0 0 1657 1600 1.163 .86 .752 .775 .877 1.777 32 170 1.039 .95 60 3330 9020 43 49 142 148 0 1205 415 790 .886 1124 708 1.128 .776 -.174 -.366 -.366
9 848 688 380 367 468 321 795 657 422 386 415 290 0 0 239 205 254 155 82 80 34 44 789 705 1.458 .686 .699 .69 .708 2.017 52 285 .636 .57 80 3480 9030 43 51 156 164 0 709 378 331 .707 677 299 1.414 .72 -.5 -.473 -.473
10 946 830 342 355 604 475 937 754 376 363 595 399 0 0 459 396 169 137 81 90 65 68 1079 994 1.272 .786 .671 .935 .914 2.604 32 198 .722 .84 70 3630 9030 43 50 171 178 0 856 366 490 .811 777 411 1.233 .691 -.303 -.533 -.533
11 830 698 347 333 483 365 792 690 377 353 445 357 0 0 320 216 160 137 92 88 63 63 848 802 1.323 .756 .802 .769 .71 2.093 80 408 .697 .67 100 3770 9030 42 52 184 194 0 720 343 376 .779 711 368 1.284 .827 -.36 -.274 -.274
12 1136 992 361 340 775 652 1149 966 385 367 788 626 0 0 215 272 132 160 100 100 100 90 1427 1414 1.189 .841 .794 .797 .877 1.476 32 213 .901 .78 70 3920 9030 43 50 200 207 0 1023 351 672 .867 996 645 1.153 .819 -.205 -.288 -.288
13 957 899 361 352 596 547 949 881 413 386 588 529 0 0 303 322 294 200 84 78 50 67 1143 1117 1.09 .918 .9 .868 .938 2.32 52 253 .778 .73 80 4070 9030 43 51 215 223 0 927 363 564 .946 908 545 1.057 .927 -.08 -.109 -.109
14 1402 1179 380 354 1022 825 1409 1212 559 516 1029 858 0 0 403 326 668 647 76 68 26 10 1847 1887 1.239 .807 .834 .802 .796 1.557 80 436 .791 .83 110 4210 9020 40 51 227 238 0 1215 365 851 .832 1249 885 1.202 .86 -.265 -.218 -.218
15 823 654 354 341 469 313 834 644 454 418 480 303 0 0 232 193 455 415 51 28 5 1 782 783 1.498 .667 .631 .703 .738 2.556 52 243 .42 .57 80 4370 9030 43 51 245 253 0 674 352 323 .688 664 312 1.453 .651 -.539 -.62 -.62
16 1978 1668 359 330 1619 1338 1996 1565 378 353 1637 1235 0 0 655 478 116 138 100 100 100 100 2957 2872 1.21 .826 .754 .834 .796 1.388 80 403 .792 .91 110 4510 9020 40 51 257 268 0 1720 340 1379 .852 1613 1273 1.174 .778 -.231 -.363 -.363
17 1531 1365 367 348 1164 1017 1563 1387 480 654 1196 1039 0 0 580 464 966 3578 63 0 10 0 2181 2235 1.145 .874 .869 .908 .88 1.66 80 365 .804 .88 110 4660 9040 42 53 272 283 0 1407 359 1048 .901 1430 1071 1.11 .896 -.151 -.159 -.159
18 402 362 354 352 48 10 368 322 396 377 14 -30 0 0 135 137 193 160 7 11 3 1 58 -16 4.8 .208 null 1.285 1.145 2.477 52 236 .731 .57 80 4800 9020 42 50 288 296 -50 373 363 10 .215 332 null 4.656 null -2.219 null
19 2205 2244 338 332 1867 1912 2154 2224 364 353 1816 1892 0 0 595 481 162 146 100 100 100 100 3779 3708 .976 1.024 1.042 1.041 1.043 1.281 52 292 .987 .94 90 4940 9020 41 50 301 310 0 2313 342 1971 1.056 2293 1951 .947 1.074 .078 .103 .103
20 939 708 333 318 606 390 877 710 347 327 544 392 0 0 404 229 121 109 93 90 81 75 996 936 1.554 .644 .721 .635 .59 2.298 80 366 .548 .71 100 5090 9020 41 51 316 326 0 730 328 402 .663 732 404 1.507 .743 -.592 -.429 -.429

Total number of rows: 43008

Table truncated, full table size 9978 Kbytes.




Supplementary data files not provided
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