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Sample GSM148724 Query DataSets for GSM148724
Status Public on Oct 03, 2007
Title PT190_5 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52831.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT190_5 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT190_5 DNA
Prostate genomic DNA; LabeledExtract: 52831.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 = 1280, 5480; 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 = 38.77; Parameter Scan Time = 10:20:49; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167388; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; 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 = 38.77; Parameter Scan Time = 10:20:49; Parameter PMT Volts = 630; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532291; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; 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/2004-06/52831.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 GPL4639
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
1 556 293 163 137 393 156 571 289 166 140 408 152 0 0 117 50 36 37 100 100 98 94 549 560 2.519 .397 .373 .399 .376 1.726 52 296 .341 .586 80 1890 6560 104 112 57 65 0 224 105 119 .303 221 116 3.302 .284 -1.723 -1.815
2 969 564 168 136 801 428 923 607 168 138 755 471 0 0 232 162 36 37 100 100 100 100 1229 1226 1.871 .534 .624 .516 .539 1.425 52 276 .54 .871 80 2040 6560 104 112 72 80 0 430 104 327 .408 463 359 2.453 .476 -1.294 -1.071
3 447 384 162 139 285 245 431 383 165 143 269 244 0 0 81 64 39 36 100 100 100 100 530 513 1.163 .86 .907 .861 .925 1.454 32 212 .864 .663 70 2180 6560 104 111 86 93 0 293 106 187 .656 292 186 1.525 .692 -.608 -.531
4 452 372 160 142 292 230 444 373 167 147 284 231 0 0 106 105 78 49 100 96 90 90 522 515 1.27 .788 .813 .767 .779 1.641 52 284 .652 .622 80 2330 6560 104 112 101 109 0 284 108 176 .601 285 176 1.664 .621 -.734 -.688
5 409 349 162 139 247 210 396 338 165 141 234 199 0 0 116 106 40 35 100 100 98 96 457 433 1.176 .85 .85 .848 .873 1.488 52 277 .851 .696 80 2480 6560 104 112 116 124 0 266 106 160 .649 258 152 1.541 .649 -.624 -.624
6 434 339 158 148 276 191 424 324 166 153 266 176 0 0 65 116 51 44 100 90 100 81 467 442 1.445 .692 .662 .601 .623 2.17 32 165 .779 .47 60 2620 6550 104 110 131 137 0 259 113 146 .528 247 134 1.894 .505 -.921 -.986
7 509 248 169 151 340 97 504 239 170 151 335 88 0 0 65 49 34 36 100 93 100 65 437 423 3.505 .285 .263 .262 .287 1.796 32 220 .267 .448 70 2770 6560 104 111 145 152 0 189 115 74 .218 182 67 4.594 .2 -2.2 -2.319
8 588 554 163 147 425 407 593 578 167 147 430 431 0 0 122 136 37 33 100 100 100 100 832 861 1.044 .958 1.002 .929 .97 1.499 32 214 .917 .776 70 2910 6550 103 110 159 166 0 423 112 311 .731 441 329 1.368 .765 -.453 -.387
9 600 763 162 150 438 613 537 733 165 153 375 583 0 0 404 181 38 38 100 100 100 100 1051 958 .715 1.4 1.555 1.557 1.535 1.45 52 304 1.046 .602 90 3050 6560 103 112 172 181 0 582 114 468 1.068 559 445 .936 1.186 .095 .246
10 728 993 172 148 556 845 740 1062 175 154 568 914 0 0 208 246 41 41 98 100 98 100 1401 1482 .658 1.52 1.609 1.601 1.582 1.52 80 344 1.162 .924 100 3200 6560 103 113 187 197 0 758 113 645 1.16 810 697 .862 1.228 .214 .296
11 464 548 176 148 288 400 459 545 184 151 283 397 0 0 77 66 65 38 100 100 100 100 688 680 .72 1.389 1.403 1.419 1.414 1.293 52 289 1.238 .662 90 3340 6560 103 112 201 210 0 418 113 305 1.06 416 303 .944 1.07 .084 .098
12 633 782 164 151 469 631 620 800 175 154 456 649 0 0 142 99 60 40 100 100 98 100 1100 1105 .743 1.345 1.423 1.403 1.362 1.371 52 324 1.31 .851 90 3490 6560 103 112 216 225 0 597 115 481 1.027 610 495 .974 1.086 .038 .119
13 670 1022 163 148 507 874 665 1041 169 152 502 893 0 0 122 142 43 38 100 100 100 100 1381 1395 .58 1.724 1.779 1.746 1.643 1.314 52 300 1.744 .867 90 3640 6550 102 111 231 240 0 780 113 667 1.315 794 681 .76 1.357 .395 .441
14 757 1012 164 152 593 860 766 1071 168 155 602 919 0 0 221 245 43 42 97 100 96 100 1453 1521 .69 1.45 1.527 1.546 1.459 1.579 80 357 1.404 .909 100 3780 6560 103 113 245 255 0 772 116 656 1.107 817 701 .904 1.165 .146 .22
15 472 563 167 150 305 413 442 562 177 162 275 412 0 0 206 111 78 87 96 97 93 96 718 687 .738 1.354 1.498 1.407 1.432 1.473 80 374 .976 .702 110 3930 6560 102 113 259 270 0 430 114 315 1.033 429 314 .968 1.143 .047 .193
16 1939 3219 162 145 1777 3074 2026 3524 171 157 1864 3379 0 0 743 1120 75 87 98 100 98 98 4851 5243 .578 1.73 1.813 1.795 1.717 1.373 80 330 1.701 .951 100 4080 6560 103 113 275 285 0 2456 111 2346 1.32 2689 2578 .758 1.383 .401 .468
17 739 1017 160 152 579 865 733 1051 163 154 573 899 0 0 131 191 36 36 100 100 100 100 1444 1472 .669 1.494 1.569 1.496 1.518 1.296 52 288 1.492 .868 90 4220 6550 102 111 289 298 0 776 116 660 1.14 802 686 .877 1.197 .189 .26
18 900 1401 156 156 744 1245 909 1441 161 156 753 1285 0 0 145 184 36 37 100 100 100 100 1989 2038 .598 1.673 1.707 1.686 1.612 1.252 52 312 1.699 .904 90 4370 6550 102 111 304 313 0 1069 119 950 1.277 1100 981 .783 1.302 .353 .381
19 1731 2689 157 150 1574 2539 1709 2706 163 156 1552 2556 0 0 336 475 44 45 100 100 100 100 4113 4108 .62 1.613 1.647 1.621 1.657 1.209 52 300 1.612 .945 90 4510 6550 102 111 318 327 0 2052 114 1937 1.231 2065 1950 .812 1.257 .3 .33
20 704 770 161 157 543 613 695 787 171 161 534 630 0 0 147 131 54 46 100 100 100 100 1156 1164 .886 1.129 1.18 1.145 1.145 1.344 52 313 1.13 .89 90 4650 6550 102 111 332 341 0 588 120 468 .861 601 481 1.161 .9 -.215 -.152

Total number of rows: 41472

Table truncated, full table size 9551 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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