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Sample GSM35662 Query DataSets for GSM35662
Status Public on May 27, 2005
Title array-CGH - GBM15
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name GBM15
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51557.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 = 34.08; Parameter Scan Time = 18:35:49; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 85442; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.11; 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 = 34.08; Parameter Scan Time = 18:35:49; Parameter PMT Volts = 720; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 154920; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; 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
1 366 211 155 .88 357 146 1.136 .824 -.184 -.28 294 321 118 185 176 136 295 313 120 198 177 128 0 0 56 81 26 67 100 82 97 42 312 305 1.294 .773 .723 .666 .712 2.649 47 282 1.252 .5 80 1350 5850 45 53 39 47 0
2 425 215 210 .439 410 195 2.276 .405 -1.186 -1.304 594 373 117 189 477 184 598 360 117 195 481 171 0 0 98 83 22 59 100 95 100 82 661 652 2.592 .386 .356 .353 .387 1.562 41 175 .379 .75 70 1500 5850 45 52 54 61 0
3 464 214 249 .554 449 235 1.804 .51 -.851 -.971 570 407 120 188 450 219 580 394 121 195 460 206 0 0 114 92 23 59 100 98 100 83 669 666 2.055 .487 .448 .46 .491 1.833 55 243 .457 .72 80 1640 5850 45 53 68 76 0
4 409 210 199 .551 404 195 1.816 .535 -.861 -.902 487 359 125 184 362 175 489 355 127 193 364 171 0 0 75 57 25 62 100 96 100 81 537 535 2.069 .483 .47 .463 .483 1.667 33 169 .467 .7 70 1800 5850 45 52 84 91 0
5 578 216 361 .624 562 345 1.603 .6 -.681 -.736 696 507 117 190 579 317 692 493 120 196 575 303 0 0 144 115 27 66 100 100 100 98 896 878 1.826 .547 .527 .54 .518 1.6 63 276 .557 .83 90 1930 5840 43 52 96 105 0
6 363 213 150 .614 361 148 1.629 .595 -.704 -.75 364 319 119 187 245 132 368 317 126 198 249 130 0 0 80 75 60 94 97 61 88 27 377 379 1.856 .539 .522 .541 .581 2.25 36 178 .578 .53 70 2070 5840 44 51 111 118 0
7 537 230 306 .663 516 286 1.508 .596 -.592 -.747 583 471 121 202 462 269 601 453 129 210 480 251 0 0 141 102 56 84 100 100 100 86 731 731 1.717 .582 .523 .571 .574 1.506 61 272 .618 .79 90 2220 5850 44 53 125 134 0
8 466 245 221 .58 444 199 1.724 .534 -.786 -.904 509 409 128 215 381 194 501 390 134 219 373 175 0 0 83 99 62 88 100 87 100 50 575 548 1.964 .509 .469 .455 .442 1.702 48 212 .7 .66 80 2370 5850 45 53 141 149 0
9 387 232 155 .608 358 125 1.646 .486 -.719 -1.042 380 340 125 204 255 136 383 314 127 208 258 110 0 0 66 88 25 60 100 80 100 46 391 368 1.875 .533 .426 .458 .459 2.219 56 234 .648 .59 90 2520 5840 43 52 155 164 0
10 489 223 265 .602 476 253 1.662 .555 -.733 -.851 565 429 124 196 441 233 580 418 128 207 456 222 0 0 166 90 29 66 100 96 100 87 674 678 1.893 .528 .487 .528 .521 2.18 63 217 .463 .69 90 2660 5840 43 52 169 178 0
11 418 239 179 .625 408 169 1.599 .587 -.677 -.768 412 367 126 210 286 157 413 358 133 223 287 148 0 0 76 85 34 71 100 84 100 54 443 435 1.822 .549 .516 .475 .545 2.105 50 238 .643 .63 80 2810 5840 44 52 185 193 0
12 483 232 251 .728 462 230 1.373 .637 -.457 -.65 474 424 130 204 344 220 491 406 134 217 361 202 0 0 82 96 32 70 100 95 97 75 564 563 1.564 .64 .56 .596 .626 1.916 48 246 .67 .71 80 2960 5840 44 52 200 208 0
13 624 244 380 1.084 600 357 .923 1.019 .116 .027 480 548 129 214 351 334 479 527 132 223 350 313 0 0 92 118 30 64 100 100 100 98 685 663 1.051 .952 .894 .934 .914 1.555 58 266 1.001 .83 90 3110 5850 44 53 214 223 0
14 625 259 367 .722 631 372 1.385 .726 -.47 -.462 643 549 135 227 508 322 648 554 137 232 513 327 0 0 96 118 30 73 100 98 100 96 830 840 1.578 .634 .637 .574 .677 2.087 57 218 .636 .72 80 3250 5840 44 52 229 237 0
15 453 270 183 .79 452 182 1.265 .789 -.339 -.342 371 398 139 237 232 161 370 397 138 247 231 160 0 0 50 65 30 92 100 83 100 32 393 391 1.441 .694 .693 .632 .757 1.854 37 142 .835 .48 70 3390 5850 45 52 243 250 0
16 1215 241 974 .921 1210 968 1.086 .782 -.119 -.355 1190 1067 132 212 1058 855 1370 1062 134 220 1238 850 0 0 477 322 27 71 100 100 100 100 1913 2088 1.237 .808 .687 .879 .844 1.503 66 352 .758 .93 100 3540 5840 43 53 257 267 0
17 809 261 548 1.038 819 558 .964 1.028 .053 .04 670 710 142 229 528 481 685 719 142 234 543 490 0 0 117 123 33 69 100 100 100 100 1009 1033 1.098 .911 .902 .902 .906 1.341 52 220 .937 .9 80 3690 5840 44 52 273 281 0
18 667 239 428 .827 648 409 1.209 .786 -.274 -.347 645 586 127 210 518 376 647 569 131 219 520 359 0 0 118 131 32 67 100 98 100 96 894 879 1.378 .726 .69 .693 .758 1.594 53 205 .725 .83 80 3830 5840 44 52 287 295 0
19 1604 218 1386 .939 1649 1432 1.065 .79 -.091 -.341 1593 1408 117 191 1476 1217 1930 1448 118 197 1813 1257 0 0 806 481 24 62 100 100 100 100 2693 3070 1.213 .825 .693 .98 .805 1.685 100 371 .747 .94 110 3980 5830 41 52 300 311 0
20 525 222 303 .698 508 286 1.432 .644 -.518 -.635 552 461 118 195 434 266 562 446 119 199 444 251 0 0 106 115 26 68 100 95 100 88 700 695 1.632 .613 .565 .559 .612 1.788 61 231 .643 .77 90 4130 5840 43 52 316 325 0

Total number of rows: 41664

Table truncated, full table size 9315 Kbytes.




Supplementary data files not provided
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