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Sample GSM35656 Query DataSets for GSM35656
Status Public on May 27, 2005
Title array-CGH - AOA6
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name AOA6
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51541.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 = 33.07; Parameter Scan Time = 17:57:03; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 84606; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.12; 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 = 33.07; Parameter Scan Time = 17:57:03; Parameter PMT Volts = 730; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 154084; 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
1 427 311 116 .443 409 98 2.258 .396 -1.175 -1.335 416 401 154 292 262 109 401 384 217 475 247 92 0 0 144 126 186 542 71 0 25 0 371 339 2.404 .416 .372 .42 .426 3.511 52 269 2.552 .69 80 1540 5780 22 30 38 46 -50
2 594 247 347 .522 574 327 1.916 .47 -.938 -1.089 793 558 128 232 665 326 823 539 143 271 695 307 0 0 144 135 64 162 100 87 100 46 991 1002 2.04 .49 .442 .461 .497 1.546 41 175 .514 .75 70 1680 5790 23 30 52 59 0
3 539 261 278 .504 519 259 1.983 .46 -.988 -1.12 680 506 129 245 551 261 691 488 137 265 562 243 0 0 137 144 39 112 100 90 100 50 812 805 2.111 .474 .432 .389 .469 2.425 51 244 .503 .73 80 1830 5790 23 31 67 75 0
4 473 259 214 .426 475 216 2.346 .413 -1.23 -1.275 629 444 127 243 502 201 650 446 134 266 523 203 0 0 118 91 46 111 100 83 100 44 703 726 2.498 .4 .388 .384 .435 1.678 36 185 .403 .68 70 1970 5790 23 30 81 88 0
5 825 239 585 .774 803 563 1.291 .714 -.369 -.487 881 775 125 225 756 550 914 754 128 236 789 529 0 0 160 155 26 74 100 100 100 100 1306 1318 1.375 .728 .67 .717 .68 1.395 63 269 .736 .9 90 2120 5790 22 31 95 104 0
6 606 246 360 .774 590 344 1.292 .692 -.37 -.532 591 569 126 231 465 338 623 554 128 236 497 323 0 0 193 107 22 70 100 100 100 100 803 820 1.376 .727 .65 .797 .756 1.953 38 173 .698 .81 70 2270 5790 23 30 111 118 0
7 643 242 401 .736 662 420 1.358 .789 -.442 -.342 671 604 126 227 545 377 659 622 128 234 533 395 0 0 150 144 22 75 100 98 100 94 922 928 1.446 .692 .741 .654 .699 1.561 59 226 .692 .85 80 2420 5780 22 30 126 134 0
8 667 251 416 .688 672 420 1.454 .671 -.54 -.577 734 627 129 236 605 391 756 631 130 244 627 395 0 0 158 128 24 74 100 100 100 96 996 1022 1.547 .646 .63 .632 .645 1.459 55 205 .643 .86 80 2560 5790 23 31 140 148 0
9 453 257 197 .529 450 194 1.889 .528 -.918 -.922 500 426 128 241 372 185 495 423 131 243 367 182 0 0 96 88 24 63 100 92 100 69 557 549 2.011 .497 .496 .455 .514 1.907 52 195 .509 .68 80 2710 5790 23 31 155 163 0
10 889 267 622 .625 906 639 1.599 .628 -.677 -.671 1123 835 129 251 994 584 1146 851 133 253 1017 600 0 0 248 192 25 69 100 100 100 100 1578 1617 1.702 .588 .59 .573 .578 1.505 58 191 .544 .86 80 2850 5790 23 31 169 177 0
11 479 272 207 .604 497 225 1.656 .614 -.728 -.705 476 450 134 256 342 194 500 467 138 265 366 211 0 0 91 100 27 77 100 87 100 69 536 577 1.763 .567 .577 .538 .586 1.932 49 230 .667 .68 80 3000 5790 23 31 184 192 0
12 502 260 243 .529 495 235 1.891 .503 -.919 -.992 590 472 131 244 459 228 599 465 133 256 468 221 0 0 122 103 23 78 100 92 100 77 687 689 2.013 .497 .472 .457 .469 1.808 54 236 .49 .69 80 3140 5780 22 30 198 206 0
13 751 279 473 .693 740 461 1.443 .668 -.529 -.582 813 706 131 262 682 444 821 695 134 256 690 433 0 0 166 154 24 73 100 100 100 100 1126 1123 1.536 .651 .628 .632 .672 1.433 61 227 .653 .89 80 3290 5780 22 30 213 221 0
14 907 297 610 .726 901 604 1.377 .711 -.462 -.492 973 852 133 279 840 573 982 846 136 282 849 567 0 0 220 183 26 77 100 100 100 100 1413 1416 1.466 .682 .668 .67 .7 1.486 64 248 .673 .89 90 3440 5780 21 30 227 236 0
15 478 297 181 .607 483 186 1.647 .584 -.72 -.776 434 449 136 279 298 170 455 454 138 283 319 175 0 0 116 123 26 80 98 73 97 52 468 494 1.753 .57 .549 .583 .617 3.206 72 319 .709 .46 100 3590 5780 21 31 242 252 0
16 2269 304 1965 .762 2281 1977 1.313 .742 -.393 -.431 2725 2132 145 286 2580 1846 2809 2143 147 288 2664 1857 0 0 741 447 30 83 100 100 100 100 4426 4521 1.398 .716 .697 .733 .722 1.264 57 219 .678 .97 80 3730 5780 22 30 257 265 0
17 1087 303 783 .858 1065 762 1.165 .863 -.221 -.212 1064 1021 151 285 913 736 1034 1001 152 292 883 716 0 0 188 192 27 88 100 100 100 100 1649 1599 1.24 .806 .811 .797 .814 1.28 55 210 .786 .93 80 3870 5780 22 30 271 279 0
18 1059 297 762 .699 1026 729 1.432 .65 -.518 -.622 1232 995 141 279 1091 716 1263 964 143 290 1122 685 0 0 266 240 25 85 100 100 100 100 1807 1807 1.524 .656 .611 .644 .631 1.428 56 246 .644 .91 90 4020 5780 21 30 285 294 0
19 3228 300 2928 1.041 3275 2975 .96 1.021 .058 .03 2952 3033 140 282 2812 2751 3054 3077 143 292 2914 2795 0 0 726 750 26 84 100 100 100 100 5563 5709 1.022 .978 .959 .985 .98 1.287 74 234 .964 .97 90 4160 5780 21 30 299 308 0
20 647 291 357 .658 618 328 1.52 .591 -.604 -.759 674 608 132 273 542 335 687 581 136 287 555 308 0 0 149 121 24 83 100 100 100 95 877 863 1.618 .618 .555 .605 .606 1.64 65 249 .624 .76 90 4310 5780 21 30 314 323 0

Total number of rows: 41664

Table truncated, full table size 9627 Kbytes.




Supplementary data files not provided
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