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Sample GSM148741 Query DataSets for GSM148741
Status Public on Oct 03, 2007
Title PT87_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48744.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT87_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT87_1 DNA
Prostate genomic DNA; LabeledExtract: 48744.Channel_2
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe
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 = 39.05; Parameter Scan Time = 11:39:58; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe
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 = 39.05; Parameter Scan Time = 11:39:58; Parameter PMT Volts = 670; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512818; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.07; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe
Description Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48744.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 06, 2006
Last update date Oct 03, 2007
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL4640
Series (1)
GSE6469 Array CGH data of 64 prostate cancer specimens

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
LOG_RAT2N_MEAN 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
VALUE 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

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 LOG_RAT2N_MEAN VALUE
1 500 434 135 120 365 314 521 401 139 125 386 281 0 0 133 167 41 37 100 100 98 98 679 667 1.162 .86 .728 .803 .851 1.646 52 300 .919 .789 80 1640 6030 79 87 84 92 0 438 121 317 .868 404 283 1.153 .734 -.205 -.446
2 920 500 138 118 782 382 936 536 140 127 798 418 0 0 181 133 32 66 100 100 100 96 1164 1216 2.047 .488 .524 .466 .494 1.44 32 210 .479 .81 70 1770 6030 79 86 97 104 0 504 119 385 .493 541 422 2.03 .528 -1.021 -.921
3 811 642 139 121 672 521 864 656 140 130 725 535 0 0 198 180 33 61 100 100 100 98 1193 1260 1.29 .775 .738 .763 .755 1.487 52 287 .76 .868 80 1920 6030 79 87 112 120 0 647 122 525 .782 662 540 1.279 .744 -.355 -.426
4 931 414 137 128 794 286 953 406 139 132 816 278 0 0 180 109 33 39 100 100 100 100 1080 1094 2.776 .36 .341 .342 .361 1.449 32 216 .329 .744 70 2060 6030 79 86 126 133 0 418 129 288 .363 409 280 2.753 .344 -1.461 -1.541
5 852 716 132 121 720 595 852 712 138 125 720 591 0 0 229 250 33 39 100 98 100 96 1315 1311 1.21 .826 .821 .756 .824 1.543 52 342 .874 .898 90 2210 6020 77 86 140 149 0 722 122 600 .833 718 596 1.2 .828 -.263 -.273
6 723 414 139 127 584 287 742 422 143 129 603 295 0 0 128 96 31 39 100 100 100 96 871 898 2.035 .491 .489 .47 .507 1.579 32 214 .482 .749 70 2350 6030 79 86 155 162 0 418 128 289 .496 426 297 2.018 .493 -1.013 -1.019
7 661 726 138 130 523 596 701 723 141 136 563 593 0 0 151 147 34 44 100 100 100 100 1119 1156 .878 1.14 1.053 1.169 1.147 1.375 52 288 1.135 .869 80 2500 6030 79 87 170 178 0 732 131 601 1.149 729 598 .87 1.062 .201 .087
8 619 639 140 121 479 518 633 630 145 130 493 509 0 0 174 191 35 42 100 100 96 100 997 1002 .925 1.081 1.032 1.124 1.088 1.593 52 264 1.101 .842 80 2650 6030 79 87 185 193 0 644 122 522 1.091 635 513 .917 1.041 .125 .058
9 528 576 136 124 392 452 517 580 137 127 381 456 0 0 118 157 32 39 100 100 100 98 844 837 .867 1.153 1.197 1.122 1.198 1.474 52 303 1.185 .804 90 2800 6030 78 87 199 208 0 581 125 456 1.163 585 460 .86 1.207 .218 .271
10 791 694 133 128 658 566 801 684 133 131 668 556 0 0 148 183 32 43 100 100 100 100 1224 1224 1.163 .86 .832 .836 .85 1.334 52 303 .897 .85 90 2940 6020 77 86 213 222 0 700 129 571 .867 690 561 1.153 .839 -.205 -.253
11 507 489 132 125 375 364 519 490 135 129 387 365 0 0 118 119 32 41 98 100 98 100 739 752 1.03 .971 .943 1.008 .923 1.803 52 277 .99 .779 80 3090 6030 79 87 229 237 0 493 126 367 .979 494 368 1.022 .951 -.031 -.072
12 506 542 137 130 369 412 508 518 140 133 371 388 0 0 127 116 35 40 100 100 98 100 781 759 .896 1.117 1.046 1.159 1.162 1.471 52 266 1.091 .818 80 3240 6030 79 87 244 252 0 547 131 415 1.126 522 391 .888 1.055 .171 .077
13 558 659 138 136 420 523 555 679 142 140 417 543 0 0 110 140 40 44 100 100 100 100 943 960 .803 1.245 1.302 1.226 1.262 1.287 52 307 1.28 .866 90 3380 6020 77 86 257 266 0 665 137 527 1.256 685 548 .796 1.313 .329 .393
14 675 815 142 131 533 684 676 833 143 133 534 702 0 0 163 172 31 40 100 100 100 100 1217 1236 .779 1.283 1.315 1.338 1.216 1.456 52 316 1.258 .883 90 3530 6030 78 87 272 281 0 822 132 690 1.294 840 708 .773 1.326 .372 .407
15 460 497 141 136 319 361 469 485 142 141 328 349 0 0 82 117 31 40 100 100 100 100 680 677 .884 1.132 1.064 1.115 1.172 1.471 52 254 1.164 .756 80 3670 6030 79 87 287 295 0 501 137 364 1.141 489 352 .876 1.073 .191 .102
16 1058 1431 138 131 920 1300 999 1340 141 135 861 1209 0 0 471 570 33 38 98 100 98 100 2220 2070 .708 1.413 1.404 1.546 1.376 1.711 52 328 1.373 .948 90 3820 6030 78 87 301 310 0 1443 132 1311 1.425 1351 1219 .702 1.416 .511 .502
17 755 532 134 128 621 404 737 528 139 130 603 400 0 0 157 168 34 38 100 100 100 98 1025 1003 1.537 .651 .663 .606 .614 1.406 52 264 .694 .86 80 3970 6020 78 86 317 325 0 537 129 407 .656 532 403 1.524 .669 -.608 -.58
18 730 780 132 128 598 652 719 826 138 132 587 698 0 0 169 203 33 38 100 100 100 100 1250 1285 .917 1.09 1.189 1.068 1.165 1.391 52 258 1.104 .887 80 4120 6020 78 86 332 340 0 787 129 658 1.1 833 704 .909 1.199 .137 .262
19 1495 1584 141 131 1354 1453 1437 1589 144 133 1296 1458 0 0 320 419 32 39 100 100 100 100 2807 2754 .932 1.073 1.125 1.047 1.077 1.24 52 316 1.098 .944 90 4260 6020 77 86 345 354 0 1597 132 1465 1.082 1602 1470 .924 1.135 .114 .182
20 704 586 142 130 562 456 706 589 144 131 564 459 0 0 143 146 33 39 100 100 100 98 1018 1023 1.232 .811 .814 .78 .845 1.399 52 328 .836 .856 90 4410 6020 77 86 360 369 0 591 131 460 .818 594 463 1.222 .821 -.289 -.285

Total number of rows: 41664

Table truncated, full table size 9382 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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