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Sample GSM148761 Query DataSets for GSM148761
Status Public on Oct 03, 2007
Title PT180_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47168.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT180_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT180_2 DNA
Prostate genomic DNA; LabeledExtract: 47168.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 = 1120, 5530; 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 = 39.34; Parameter Scan Time = 12:14:36; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135373; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; 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 = 39.34; Parameter Scan Time = 12:14:36; Parameter PMT Volts = 690; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.05; 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/2003-12/47168.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
1 626 473 138 153 488 320 628 460 142 160 490 307 0 0 92 94 32 52 100 100 100 98 808 797 1.525 .656 .627 .637 .686 1.444 52 344 .641 .709 90 1800 5980 40 49 63 72 0 566 183 383 .785 551 368 1.274 .75 -.349 -.415
2 901 489 137 155 764 334 944 492 141 161 807 337 0 0 201 139 32 47 100 100 100 94 1098 1144 2.287 .437 .418 .411 .43 1.485 52 266 .434 .784 80 1950 5980 41 49 79 87 0 585 186 400 .523 589 403 1.911 .5 -.934 -1
3 1167 574 139 154 1028 420 1061 540 141 158 922 386 0 0 330 180 32 49 100 100 100 98 1448 1308 2.448 .409 .419 .388 .407 1.417 52 301 .412 .84 90 2090 5980 40 49 92 101 0 687 184 503 .489 646 462 2.044 .501 -1.032 -.996
4 746 385 137 148 609 237 784 397 137 150 647 249 0 0 210 110 33 47 100 96 100 88 846 896 2.57 .389 .385 .373 .392 1.538 52 242 .377 .754 80 2240 5980 41 49 108 116 0 461 177 284 .466 475 298 2.146 .461 -1.102 -1.118
5 1123 790 135 150 988 640 1135 767 139 149 1000 617 0 0 287 218 34 48 100 100 100 100 1628 1617 1.544 .648 .617 .645 .648 1.438 80 358 .656 .898 100 2380 5980 40 50 121 131 0 946 180 766 .776 918 739 1.289 .739 -.367 -.437
6 633 385 135 148 498 237 645 404 139 149 510 256 0 0 158 110 32 47 100 94 100 90 735 766 2.101 .476 .502 .432 .468 1.666 52 244 .486 .746 80 2530 5980 41 49 137 145 0 461 177 284 .57 484 306 1.755 .601 -.812 -.735
7 976 698 135 149 841 549 965 683 140 156 830 534 0 0 113 127 33 50 100 100 100 100 1390 1364 1.532 .653 .643 .641 .643 1.289 52 277 .646 .847 90 2670 5980 40 49 150 159 0 836 178 657 .782 818 639 1.28 .77 -.356 -.377
8 865 610 134 149 731 461 866 593 138 154 732 444 0 0 132 110 31 50 100 100 100 100 1192 1176 1.586 .631 .607 .625 .614 1.289 52 295 .592 .825 90 2810 5980 40 49 164 173 0 730 178 552 .755 710 532 1.324 .726 -.405 -.462
9 690 478 138 143 552 335 693 475 141 152 555 332 0 0 93 97 32 50 100 98 100 98 887 887 1.648 .607 .598 .583 .592 1.433 52 311 .631 .793 90 2970 5970 39 48 180 189 0 572 171 401 .727 569 397 1.376 .716 -.461 -.482
10 1087 706 141 148 946 558 1077 720 144 152 936 572 0 0 141 155 31 52 100 100 100 100 1504 1508 1.695 .59 .611 .57 .604 1.331 52 301 .589 .86 90 3110 5970 39 48 194 203 0 845 177 668 .706 862 685 1.416 .732 -.502 -.451
11 578 441 143 145 435 296 591 430 146 148 448 285 0 0 91 100 31 47 100 100 100 100 731 733 1.47 .68 .636 .661 .673 1.484 52 308 .682 .753 90 3260 5980 40 49 209 218 0 528 174 354 .815 515 341 1.228 .762 -.296 -.393
12 773 510 142 138 631 372 773 510 146 145 631 372 0 0 114 109 31 49 100 100 100 100 1003 1003 1.696 .59 .59 .572 .586 1.375 52 325 .605 .778 90 3410 5970 39 48 224 233 0 611 165 445 .706 611 445 1.417 .706 -.503 -.503
13 830 628 143 141 687 487 822 616 145 146 679 475 0 0 128 112 31 49 100 100 100 98 1174 1154 1.411 .709 .7 .697 .691 1.31 52 288 .723 .864 90 3550 5970 39 48 238 247 0 752 169 583 .849 737 569 1.178 .838 -.237 -.256
14 870 605 140 143 730 462 904 618 142 145 764 475 0 0 178 152 32 43 100 98 100 97 1192 1239 1.58 .633 .622 .604 .638 1.34 80 370 .642 .877 100 3700 5970 39 49 253 263 0 724 171 553 .758 740 569 1.32 .744 -.4 -.426
15 574 409 141 140 433 269 573 412 144 142 432 272 0 0 74 80 35 42 100 100 100 100 702 704 1.61 .621 .63 .603 .651 1.444 52 289 .651 .736 90 3850 5970 39 48 268 277 0 490 168 322 .744 493 326 1.345 .754 -.427 -.408
16 2031 1538 143 143 1888 1395 2093 1575 147 148 1950 1432 0 0 405 309 36 44 100 100 100 100 3283 3382 1.353 .739 .734 .737 .732 1.206 52 326 .739 .934 90 3990 5970 39 48 282 291 0 1841 171 1670 .885 1886 1714 1.13 .879 -.177 -.186
17 973 729 145 141 828 588 969 745 148 146 824 604 0 0 147 132 35 45 100 100 100 100 1416 1428 1.408 .71 .733 .701 .694 1.286 52 296 .722 .849 90 4150 5970 39 48 298 307 0 873 169 704 .85 892 723 1.176 .878 -.234 -.188
18 924 714 138 137 786 577 944 713 144 143 806 576 0 0 145 127 34 47 100 100 100 100 1363 1382 1.362 .734 .715 .73 .741 1.249 52 276 .719 .878 90 4280 5970 39 48 311 320 0 855 164 691 .879 854 690 1.138 .856 -.186 -.225
19 2045 1316 141 137 1904 1179 1886 1064 146 141 1745 927 0 0 850 670 35 45 100 100 100 100 3083 2672 1.615 .619 .531 .609 .568 1.483 80 352 .648 .916 100 4440 5970 39 49 327 337 0 1576 164 1412 .741 1274 1110 1.349 .636 -.432 -.653
20 786 493 138 131 648 362 806 495 150 140 668 364 0 0 130 102 168 76 100 98 95 96 1010 1032 1.79 .559 .545 .544 .558 1.351 80 352 .469 .637 100 4580 5970 39 49 341 351 0 590 157 433 .669 593 436 1.495 .652 -.58 -.616

Total number of rows: 41664

Table truncated, full table size 9430 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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