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Sample GSM35652 Query DataSets for GSM35652
Status Public on May 27, 2005
Title array-CGH - AOA2
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name AOA2
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51553.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 = 32.03; Parameter Scan Time = 16:11:37; Parameter PMT Volts = 510; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 85298; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.17; 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 = 32.03; Parameter Scan Time = 16:11:37; Parameter PMT Volts = 710; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 154776; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; 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
1 370 250 119 .451 364 114 2.218 .442 -1.149 -1.18 425 331 160 224 265 107 418 326 163 231 258 102 0 0 107 94 30 67 100 62 97 35 372 360 2.477 .404 .395 .38 .404 2.97 67 405 .46 .37 100 1740 6730 44 54 33 43 0
2 558 265 294 .574 488 223 1.743 .468 -.802 -1.095 681 500 169 237 512 263 646 437 171 246 477 200 0 0 212 308 31 73 100 91 100 72 775 677 1.947 .514 .419 .377 .409 2.241 47 224 .74 .7 80 1880 6730 45 53 48 56 0
3 553 268 285 .686 542 274 1.457 .638 -.543 -.649 579 495 164 240 415 255 593 485 165 242 429 245 0 0 91 121 28 63 100 97 100 85 670 674 1.627 .614 .571 .551 .588 1.837 70 251 .689 .78 90 2020 6730 44 53 61 70 0
4 446 261 184 .452 424 163 2.214 .411 -1.147 -1.284 575 399 167 234 408 165 564 380 171 238 397 146 0 0 152 173 30 65 100 77 100 50 573 543 2.473 .404 .368 .423 .367 2.139 40 219 .457 .48 80 2170 6740 46 54 77 85 0
5 651 262 389 .743 622 360 1.346 .661 -.428 -.597 686 583 163 235 523 348 707 557 176 266 544 322 0 0 112 140 174 361 98 40 91 2 871 866 1.503 .665 .592 .63 .63 1.608 85 336 1.511 .8 100 2320 6730 44 54 91 101 0
6 325 252 73 .406 327 75 2.466 .388 -1.302 -1.367 337 291 158 226 179 65 351 293 158 234 193 67 0 0 76 86 26 63 96 50 88 25 244 260 2.754 .363 .347 .525 .516 3.502 52 227 .554 .27 80 2460 6730 45 53 106 114 -50
7 616 267 350 .838 623 356 1.193 .854 -.255 -.227 578 552 161 239 417 313 578 558 164 247 417 319 0 0 88 126 25 72 100 100 100 88 730 736 1.332 .751 .765 .702 .736 1.606 72 241 .821 .81 90 2610 6730 44 53 120 129 0
8 520 276 245 .55 490 214 1.82 .496 -.864 -1.011 612 466 167 247 445 219 599 439 190 254 432 192 0 0 129 159 87 78 100 81 97 67 664 624 2.032 .492 .444 .429 .471 2.023 70 306 .593 .69 100 2760 6740 45 55 135 145 0
9 1982 376 1606 2.331 533 156 .429 .471 1.221 -1.086 928 1775 239 337 689 1438 571 477 282 328 332 140 0 0 896 3391 140 102 100 69 76 30 2127 472 .479 2.087 .422 .519 .524 3.311 13 63 4.103 .78 50 2930 6720 45 50 154 159 0
10 657 269 388 .76 657 388 1.316 .744 -.396 -.427 675 588 165 241 510 347 686 588 189 272 521 347 0 0 132 118 84 134 100 95 98 74 857 868 1.47 .68 .666 .665 .652 1.698 74 297 .724 .71 100 3040 6730 44 54 163 173 0
11 404 255 150 .54 414 160 1.851 .57 -.888 -.81 440 362 163 228 277 134 443 371 164 238 280 143 0 0 64 76 25 66 100 80 100 54 411 423 2.067 .484 .511 .427 .525 2.269 68 237 .553 .64 90 3190 6730 44 53 178 187 0
12 471 255 217 .833 472 218 1.2 .789 -.263 -.342 420 422 160 228 260 194 436 423 161 231 276 195 0 0 93 108 24 61 100 89 97 71 454 471 1.34 .746 .707 .715 .745 2.384 77 302 .872 .65 100 3340 6730 44 54 193 203 0
13 530 267 264 .686 528 261 1.457 .682 -.543 -.552 544 475 160 239 384 236 543 473 163 238 383 234 0 0 61 96 25 64 100 95 100 87 620 617 1.627 .615 .611 .558 .625 1.645 71 211 .654 .78 90 3480 6730 44 53 207 216 0
14 828 274 554 1.095 830 556 .914 1.049 .13 .069 670 741 164 245 506 496 694 743 166 248 530 498 0 0 138 132 25 69 100 100 100 100 1002 1028 1.02 .98 .94 .99 .999 1.479 84 286 .986 .88 100 3630 6730 44 54 222 232 0
15 399 287 112 .463 390 103 2.158 .43 -1.11 -1.218 410 357 169 257 241 100 408 349 173 266 239 92 0 0 51 64 30 70 100 67 100 28 341 331 2.41 .415 .385 .36 .419 2.658 52 205 .538 .31 90 3780 6730 44 53 237 246 0
16 1108 266 842 .875 1061 795 1.142 .774 -.192 -.369 1127 992 165 238 962 754 1192 950 167 252 1027 712 0 0 238 222 30 97 100 100 100 100 1716 1739 1.276 .784 .693 .779 .773 1.316 74 287 .779 .94 100 3920 6730 44 54 251 261 0
17 587 264 324 .666 596 333 1.501 .662 -.586 -.596 651 526 165 236 486 290 668 534 166 245 503 298 0 0 120 124 26 100 100 94 100 77 776 801 1.676 .597 .592 .554 .587 1.689 74 261 .629 .79 100 4070 6730 44 54 266 276 0
18 698 264 434 .86 675 411 1.162 .784 -.217 -.351 671 625 166 236 505 389 690 604 167 237 524 368 0 0 122 144 25 64 98 100 98 97 894 892 1.298 .77 .702 .761 .702 1.809 77 243 .822 .82 100 4220 6730 44 54 281 291 0
19 3097 268 2829 1.428 2941 2673 .7 1.311 .514 .391 2148 2773 167 240 1981 2533 2206 2634 168 245 2039 2394 0 0 764 1229 24 65 100 100 100 100 4514 4433 .782 1.279 1.174 1.3 1.186 1.885 93 278 1.366 .93 110 4360 6730 43 54 294 305 0
20 594 262 332 .833 599 336 1.2 .798 -.263 -.325 563 532 165 235 398 297 586 536 166 240 421 301 0 0 104 99 26 64 100 100 100 92 695 722 1.34 .746 .715 .732 .753 1.624 85 299 .777 .78 110 4500 6730 43 54 308 319 0

Total number of rows: 41664

Table truncated, full table size 9330 Kbytes.




Supplementary data files not provided
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