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Sample GSM40624 Query DataSets for GSM40624
Status Public on Jan 27, 2006
Title array-CGH LXR-Mock
Sample type genomic
 
Channel 1
Source name Cy3: male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name Cy5: LXR-Mock
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-07/54379.gif
Sample_scan_protocol: Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 34.72; Parameter Scan Time = 16:14:58; Parameter PMT Volts = 600; Parameter Scan Date = 2004-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 77409; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.06; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
Sample_scan_protocol: Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 34.72; Parameter Scan Time = 16:14:58; Parameter PMT Volts = 730; Parameter Scan Date = 2004-03-04; Parameter Pixel Size = 10; Parameter Laser on time = 146910; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.61; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
 
Submission date Feb 01, 2005
Last update date Mar 24, 2006
Contact name Markus Bredel
E-mail(s) [email protected]
Phone 650-498-6012
Organization name Stanford University School of Medicine
Street address
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1831
Series (1)
GSE2221 Drug resistance in glioblastoma

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 922 855 527 667 395 188 873 851 531 673 346 184 0 0 201 136 89 126 98 73 87 31 583 530 2.101 .476 .532 .5 .558 2.673 90 480 .398 .33 120 1800 6080 26 38 18 30 0 1166 910 256 .649 1161 251 1.54 .725 -.623 -.463 -.623
2 1100 951 523 657 577 294 958 948 532 670 435 291 0 0 394 208 102 150 100 74 93 48 871 726 1.963 .51 .669 .53 .645 3.339 113 277 .348 .48 120 1950 6080 26 38 33 45 0 1297 896 401 .695 1293 397 1.439 .912 -.525 -.132 -.525
3 1265 1184 517 643 748 541 1092 1160 529 656 575 517 0 0 459 206 103 155 100 98 97 87 1289 1092 1.383 .723 .899 .786 .834 1.867 108 283 .57 .74 120 2090 6080 26 38 47 59 0 1615 877 738 .987 1582 705 1.014 1.226 -.02 .294 -.02
4 747 803 524 628 223 175 719 766 527 633 195 138 0 0 199 238 87 130 77 53 57 25 398 333 1.274 .785 .708 .925 1.034 3.216 156 326 1.024 .72 140 2230 6110 28 42 60 74 -50 1095 857 239 1.07 1045 188 .934 .965 -.051 .098
5 729 714 519 605 210 109 733 710 522 610 214 105 0 0 133 152 83 124 81 44 58 16 319 319 1.927 .519 .491 .725 .782 3.551 156 421 1.066 .25 140 2380 6080 25 39 75 89 -50 974 825 149 .708 968 143 1.412 .669 -.579 -.498
6 1497 1356 516 611 981 745 1293 1322 522 616 777 711 0 0 584 268 84 125 100 99 99 97 1726 1488 1.317 .759 .915 .845 .753 1.774 126 249 .594 .83 120 2520 6080 26 38 90 102 0 1850 833 1016 1.036 1803 970 .965 1.248 .051 .32 .051
7 606 678 506 631 100 47 606 673 508 633 100 42 0 0 108 142 88 128 53 30 24 8 147 142 2.128 .47 .42 .989 .977 4.161 156 429 3.357 .19 140 2670 6070 24 38 104 118 -50 925 861 64 .641 918 57 1.56 .573 -.804 -.641
8 1540 1256 503 649 1037 607 1427 1256 516 660 924 607 0 0 444 243 96 133 100 100 100 92 1644 1531 1.708 .585 .657 .578 .594 1.838 114 259 .477 .72 120 2820 6080 26 38 120 132 0 1713 885 828 .798 1713 828 1.253 .896 -.325 -.158 -.325
9 1387 959 510 634 877 325 1391 950 524 650 881 316 0 0 248 154 95 132 100 89 99 64 1202 1197 2.698 .371 .359 .342 .356 1.951 128 250 .315 .63 120 2970 6080 26 38 135 147 0 1308 865 443 .505 1296 431 1.978 .489 -.984 -1.031 -.984
10 2697 1671 531 610 2166 1061 2781 1671 537 632 2250 1061 0 0 567 295 91 139 100 100 100 100 3227 3311 2.041 .49 .472 .491 .487 1.292 127 234 .452 .93 120 3110 6080 26 38 149 161 0 2279 832 1447 .668 2279 1447 1.497 .643 -.582 -.637 -.582
11 1032 811 527 581 505 230 1030 798 531 589 503 217 0 0 135 180 88 121 100 68 98 45 735 720 2.196 .455 .431 .369 .468 3.051 131 279 .404 .43 130 3260 6080 25 38 163 176 0 1106 792 314 .621 1088 296 1.61 .588 -.687 -.765 -.687
12 1742 987 520 616 1222 371 1744 955 529 620 1224 339 0 0 322 202 89 118 100 91 100 75 1593 1563 3.294 .304 .277 .276 .305 1.828 120 253 .281 .72 120 3400 6080 26 38 178 190 0 1346 840 506 .414 1303 462 2.415 .378 -1.272 -1.404 -1.272
13 1462 1064 530 637 932 427 1463 1041 532 648 933 404 0 0 264 250 91 126 100 93 100 72 1359 1337 2.183 .458 .433 .411 .436 2.097 133 284 .428 .66 130 3550 6080 25 38 192 205 0 1451 869 582 .625 1420 551 1.6 .591 -.678 -.76 -.678
14 2001 1398 556 665 1445 733 2049 1363 566 678 1493 698 0 0 351 224 127 142 100 100 100 99 2178 2191 1.971 .507 .468 .501 .482 1.523 139 324 .452 .82 130 3690 6070 24 37 206 219 0 1907 907 1000 .692 1859 952 1.445 .638 -.531 -.649 -.531
15 1027 1096 554 674 473 422 1021 1089 571 690 467 415 0 0 132 226 129 134 100 90 92 76 895 882 1.121 .892 .889 .821 .898 1.996 52 327 .805 .69 130 3840 6070 24 37 221 234 0 1495 919 576 1.217 1485 566 .822 1.212 .283 .278 .283
16 4993 3121 549 655 4444 2466 5143 3181 564 675 4594 2526 0 0 1549 582 122 128 100 100 100 100 6910 7120 1.802 .555 .55 .582 .534 1.343 130 330 .506 .96 130 3990 6070 24 37 236 249 0 4257 893 3364 .757 4339 3445 1.321 .75 -.402 -.415 -.402
17 1911 1314 536 682 1375 632 1942 1303 545 688 1406 621 0 0 383 206 102 130 100 100 100 99 2007 2027 2.176 .46 .442 .456 .438 1.562 123 270 .425 .84 120 4130 6070 25 37 251 263 0 1792 930 862 .627 1777 847 1.595 .602 -.674 -.731 -.674
18 2889 1824 545 682 2344 1142 2960 1839 552 689 2415 1157 0 0 603 246 100 142 100 100 100 100 3486 3572 2.053 .487 .479 .494 .468 1.352 127 264 .448 .92 120 4280 6070 25 37 266 278 0 2488 930 1558 .665 2508 1578 1.505 .653 -.59 -.614 -.59
19 5506 3498 543 671 4963 2827 5437 3347 550 674 4894 2676 0 0 1673 825 100 136 100 100 100 100 7790 7570 1.756 .57 .547 .583 .573 1.268 123 266 .54 .97 120 4420 6070 25 37 280 292 0 4771 915 3856 .777 4565 3650 1.287 .746 -.364 -.423 -.364
20 1730 1180 531 671 1199 509 1743 1162 532 674 1212 491 0 0 284 182 93 129 100 100 100 93 1708 1703 2.356 .425 .405 .411 .411 1.686 127 317 .373 .74 130 4570 6070 24 37 294 307 0 1610 915 694 .579 1585 670 1.727 .553 -.788 -.856 -.788

Total number of rows: 41472

Table truncated, full table size 9852 Kbytes.




Supplementary data files not provided
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