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Sample GSM35648 Query DataSets for GSM35648
Status Public on May 27, 2005
Title array-CGH - AO1
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name AO1
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51547.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 33.22; Parameter Scan Time = 18:27:41; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 84637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 33.22; Parameter Scan Time = 18:27:41; Parameter PMT Volts = 710; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 154115; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
 
Submission date Nov 19, 2004
Last update date May 29, 2005
Contact name Markus Bredel
E-mail(s) mbredel@stanford.edu
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 GPL1715
Series (1)
GSE1991 Array-CGH in human glial brain tumors

Data table header descriptions
ID_REF ID_REF
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 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
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
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

Data table
ID_REF CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN 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
1 631 275 357 .726 602 327 1.377 .617 -.461 -.697 622 616 131 268 491 348 661 587 138 284 530 319 0 0 134 169 35 91 100 98 100 86 839 849 1.411 .709 .602 .66 .7 1.556 51 318 .775 .78 90 1440 6740 37 46 27 36 0
2 771 283 488 .604 763 480 1.656 .59 -.728 -.761 942 752 134 276 808 476 947 744 138 287 813 468 0 0 161 122 29 74 100 100 100 100 1284 1281 1.697 .589 .576 .583 .586 1.291 46 236 .581 .91 80 1580 6730 37 45 42 50 0
3 707 286 421 .559 712 426 1.79 .572 -.84 -.805 887 690 133 279 754 411 878 695 135 281 745 416 0 0 224 134 27 70 100 100 100 100 1165 1161 1.835 .545 .558 .541 .506 1.581 65 272 .524 .83 90 1720 6730 36 45 55 64 0
4 642 280 362 .725 627 347 1.379 .664 -.464 -.59 631 626 132 273 499 353 655 612 133 274 523 339 0 0 137 128 24 71 100 97 100 95 852 862 1.414 .707 .648 .696 .607 1.593 47 143 .724 .8 70 1870 6730 37 44 71 78 0
5 850 268 582 .73 851 583 1.369 .644 -.453 -.634 927 829 130 261 797 568 1035 830 132 271 905 569 0 0 300 169 24 76 100 100 100 100 1365 1474 1.403 .713 .629 .74 .688 1.467 102 368 .667 .9 110 2020 6720 34 45 84 95 0
6 591 277 315 .72 586 310 1.389 .697 -.474 -.52 567 577 130 270 437 307 574 572 133 280 444 302 0 0 108 99 23 76 100 100 100 94 744 746 1.423 .703 .68 .688 .704 1.531 38 145 .684 .76 70 2160 6730 37 44 100 107 0
7 698 272 426 .664 691 419 1.506 .644 -.59 -.635 777 681 135 265 642 416 786 674 137 273 651 409 0 0 171 121 26 69 100 100 100 100 1058 1060 1.543 .648 .628 .645 .619 1.417 62 237 .635 .88 90 2310 6730 36 45 114 123 0
8 757 275 483 .777 755 481 1.286 .727 -.363 -.459 756 739 135 268 621 471 796 737 135 277 661 469 0 0 231 153 24 69 100 100 100 98 1092 1130 1.318 .758 .71 .781 .759 1.624 79 301 .695 .86 100 2450 6720 35 45 128 138 0
9 548 276 273 .536 549 274 1.867 .55 -.901 -.864 641 535 132 269 509 266 630 536 132 284 498 267 0 0 135 129 23 78 100 93 100 78 775 765 1.914 .523 .536 .482 .536 1.746 60 214 .521 .77 90 2590 6730 36 45 142 151 0
10 853 274 579 .661 826 552 1.513 .634 -.597 -.657 1010 832 134 267 876 565 1005 806 135 278 871 539 0 0 338 293 25 69 100 100 100 100 1441 1410 1.55 .645 .619 .625 .647 1.517 64 209 .651 .88 90 2750 6730 36 45 158 167 0
11 532 285 247 .564 528 243 1.773 .539 -.826 -.893 573 519 135 278 438 241 586 515 134 280 451 237 0 0 115 117 23 66 100 94 100 82 679 688 1.817 .55 .525 .492 .484 1.916 57 242 .575 .76 90 2880 6730 36 45 171 180 0
12 606 286 320 .587 580 294 1.704 .54 -.769 -.89 674 591 129 279 545 312 674 566 130 287 545 287 0 0 171 114 22 74 100 100 100 93 857 832 1.747 .572 .527 .565 .539 1.532 58 254 .56 .81 90 3030 6730 36 45 186 195 0
13 834 284 550 .746 836 552 1.341 .765 -.423 -.386 868 814 130 277 738 537 852 816 131 284 722 539 0 0 155 161 22 69 100 100 100 100 1275 1261 1.374 .728 .747 .706 .708 1.309 65 238 .748 .92 90 3180 6720 35 44 201 210 0
14 925 282 643 .779 913 631 1.284 .77 -.36 -.377 956 902 131 275 825 627 951 891 133 280 820 616 0 0 218 180 25 71 100 100 100 100 1452 1436 1.316 .76 .751 .76 .737 1.349 70 232 .742 .9 90 3320 6720 35 44 215 224 0
15 417 287 130 .489 386 99 2.043 .381 -1.031 -1.392 397 407 131 280 266 127 392 377 134 283 261 97 0 0 81 106 52 79 100 56 100 27 393 358 2.094 .477 .372 .414 .409 2.444 69 300 .65 .42 100 3460 6720 35 45 229 239 0
16 2136 286 1850 .821 2254 1968 1.218 .713 -.285 -.487 2388 2084 134 279 2254 1805 2893 2199 138 286 2759 1920 0 0 1288 789 53 85 100 100 100 100 4059 4679 1.249 .801 .696 .935 .797 1.645 83 320 .73 .96 110 3630 6730 35 46 245 256 0
17 1062 280 782 .894 1049 769 1.119 .836 -.162 -.259 1008 1036 133 273 875 763 1053 1023 136 283 920 750 0 0 298 270 30 80 100 100 100 100 1638 1670 1.147 .872 .815 .875 .867 1.435 66 335 .903 .89 110 3750 6720 34 45 257 268 0
18 1102 280 822 .781 1082 803 1.281 .74 -.357 -.435 1182 1075 129 273 1053 802 1214 1056 834 1309 1085 783 0 0 312 243 3608 5001 0 0 0 0 1855 1868 1.313 .762 .722 .768 .758 1.286 65 228 .754 .93 90 3900 6720 35 44 273 282 0
19 2816 280 2536 .996 2865 2585 1.004 .911 -.005 -.135 2674 2747 129 273 2545 2474 2968 2795 272 520 2839 2522 0 0 1058 841 1612 2514 75 50 29 0 5019 5361 1.029 .972 .888 1.042 .912 1.447 114 370 .928 .96 120 4060 6720 34 46 288 300 0
20 824 280 544 .853 748 468 1.172 .721 -.229 -.473 771 804 133 273 638 531 783 730 136 279 650 457 0 0 182 263 26 76 100 100 100 100 1169 1107 1.202 .832 .703 .785 .727 1.82 95 307 1.131 .74 110 4190 6720 34 45 301 312 0

Total number of rows: 41664

Table truncated, full table size 9473 Kbytes.




Supplementary data files not provided
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