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Sample GSM148717 Query DataSets for GSM148717
Status Public on Oct 03, 2007
Title PT309_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47175.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT309_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT309_2 DNA
Prostate genomic DNA; LabeledExtract: 47175.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 = 880, 5320; 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 = 38.55; Parameter Scan Time = 10:31:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136037; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; 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 = 38.55; Parameter Scan Time = 10:31:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501103; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; 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/2003-12/47175.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
1 588 590 152 206 436 384 593 583 157 211 441 377 0 0 127 119 36 48 100 100 100 100 820 818 1.135 .881 .855 .88 .884 1.348 52 355 .858 .804 90 1680 5710 34 43 75 84 0 660 230 429 .985 652 422 1.016 .956 -.022 -.065
2 828 603 148 210 680 393 878 604 154 213 730 394 0 0 229 155 38 46 100 100 100 98 1073 1124 1.73 .578 .54 .567 .604 1.465 52 266 .569 .852 80 1820 5720 36 44 90 98 0 674 235 439 .646 675 441 1.548 .603 -.63 -.729
3 928 886 153 219 775 667 946 868 154 219 793 649 0 0 163 132 36 47 100 100 100 100 1442 1442 1.162 .861 .818 .865 .92 1.276 52 266 .835 .878 80 1960 5720 36 44 104 112 0 991 245 746 .962 970 726 1.039 .915 -.056 -.128
4 863 473 157 220 706 253 858 489 159 225 701 269 0 0 108 77 38 51 100 100 100 100 959 970 2.791 .358 .384 .346 .363 1.425 32 215 .345 .699 70 2110 5710 35 42 119 126 0 529 246 283 .401 547 301 2.496 .429 -1.32 -1.221
5 964 781 153 211 811 570 965 784 156 214 812 573 0 0 243 204 39 46 100 98 100 97 1381 1385 1.423 .703 .706 .663 .707 1.503 80 374 .71 .897 100 2260 5720 35 45 133 143 0 873 236 637 .786 877 641 1.273 .789 -.348 -.342
6 668 459 150 206 518 253 673 449 152 212 523 243 0 0 137 124 38 47 100 96 100 94 771 766 2.047 .488 .465 .455 .484 1.511 52 252 .505 .7 80 2400 5720 36 44 148 156 0 513 230 283 .546 502 272 1.831 .519 -.873 -.945
7 836 790 150 212 686 578 845 804 151 212 695 592 0 0 102 111 36 45 100 100 100 100 1264 1287 1.187 .843 .852 .835 .814 1.244 52 314 .835 .875 90 2550 5710 34 43 162 171 0 883 237 646 .942 899 662 1.062 .952 -.086 -.07
8 722 580 151 215 571 365 718 573 153 213 567 358 0 0 119 110 36 46 100 100 100 100 936 925 1.564 .639 .631 .622 .63 1.297 52 289 .632 .809 90 2690 5720 35 44 176 185 0 648 240 408 .715 641 400 1.399 .706 -.485 -.502
9 731 565 150 208 581 357 702 591 153 210 552 383 0 0 153 100 37 44 100 100 100 100 938 935 1.627 .614 .694 .606 .633 1.377 52 299 .603 .806 90 2840 5710 34 43 191 200 0 632 233 399 .687 661 428 1.456 .776 -.542 -.366
10 920 742 150 203 770 539 950 740 151 205 800 537 0 0 215 159 35 44 100 100 98 100 1309 1337 1.429 .7 .671 .704 .708 1.327 80 355 .684 .881 100 2990 5710 34 44 206 216 0 830 227 603 .783 827 600 1.278 .75 -.354 -.414
11 529 473 153 207 376 266 518 469 152 210 365 262 0 0 76 77 35 49 100 100 100 100 642 627 1.414 .707 .718 .691 .701 1.402 52 297 .686 .74 90 3130 5710 34 43 220 229 0 529 231 297 .791 524 293 1.264 .803 -.338 -.317
12 702 593 153 210 549 383 704 589 155 213 551 379 0 0 101 80 35 51 100 100 100 100 932 930 1.433 .698 .688 .695 .679 1.294 52 324 .684 .809 90 3280 5710 34 43 235 244 0 663 235 428 .78 659 424 1.282 .769 -.358 -.379
13 779 765 156 202 623 563 798 768 159 208 642 566 0 0 123 106 40 54 100 100 100 100 1186 1208 1.107 .904 .882 .908 .876 1.315 52 301 .886 .856 90 3420 5710 34 43 249 258 0 855 226 629 1.01 859 633 .99 .986 .015 -.021
14 849 815 149 201 700 614 876 822 155 206 727 621 0 0 184 171 39 49 100 100 100 98 1314 1348 1.14 .877 .854 .876 .878 1.38 80 390 .874 .861 100 3580 5710 34 44 265 275 0 911 225 686 .981 919 694 1.02 .955 -.028 -.066
15 521 512 147 211 374 301 508 523 150 213 361 312 0 0 88 73 37 50 100 100 100 100 675 673 1.243 .805 .864 .803 .857 1.353 52 276 .799 .723 90 3720 5710 34 43 279 288 0 572 236 337 .9 585 349 1.111 .966 -.152 -.049
16 2226 2274 149 202 2077 2072 2364 2304 151 204 2215 2102 0 0 547 446 37 47 100 100 100 100 4149 4317 1.002 .998 .949 1.022 .989 1.241 52 311 .959 .95 90 3860 5710 34 43 293 302 0 2542 226 2317 1.115 2576 2350 .897 1.061 .158 .085
17 1032 1022 148 196 884 826 1000 1023 150 197 852 827 0 0 148 143 35 45 100 100 100 100 1710 1679 1.07 .934 .971 .933 .965 1.221 52 299 .942 .918 90 4020 5710 34 43 309 318 0 1143 219 924 1.045 1144 925 .957 1.085 .063 .118
18 859 888 148 199 711 689 878 924 150 201 730 725 0 0 222 208 33 45 100 100 100 98 1400 1455 1.032 .969 .993 .984 .989 1.354 80 346 .967 .915 100 4160 5710 34 44 323 333 0 993 222 770 1.083 1033 811 .923 1.11 .116 .151
19 2594 2454 147 198 2447 2256 2614 2479 149 200 2467 2281 0 0 563 516 35 46 100 100 100 100 4703 4748 1.085 .922 .925 .923 .938 1.177 80 345 .914 .968 100 4310 5710 34 44 338 348 0 2744 221 2522 1.031 2772 2550 .97 1.034 .044 .048
20 756 581 143 199 613 382 743 582 146 203 600 383 0 0 141 113 34 47 100 100 98 98 995 983 1.605 .623 .638 .617 .615 1.46 80 346 .62 .822 100 4460 5710 34 44 353 363 0 650 222 427 .697 651 428 1.435 .714 -.521 -.487

Total number of rows: 41664

Table truncated, full table size 9568 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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