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Sample GSM148737 Query DataSets for GSM148737
Status Public on Oct 03, 2007
Title PT250_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48741.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT250_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT250_1 DNA
Prostate genomic DNA; LabeledExtract: 48741.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 = 1080, 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 = 38.74; Parameter Scan Time = 10:54:36; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; 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 = 38.74; Parameter Scan Time = 10:54:36; Parameter PMT Volts = 670; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512773; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; 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/2004-01/48741.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
1 436 467 134 144 302 323 446 459 136 144 312 315 0 0 110 127 34 42 100 100 98 98 625 627 .935 1.07 1.01 1.081 1.039 1.587 52 299 1.07 .711 80 1890 6240 100 108 77 85 0 445 137 308 1.019 438 300 .981 .962 .028 -.055
2 864 562 130 143 734 419 928 554 135 145 798 411 0 0 171 123 31 46 100 100 100 96 1153 1209 1.752 .571 .515 .558 .549 1.27 32 219 .55 .85 70 2030 6230 99 106 91 98 0 536 136 399 .544 528 392 1.838 .491 -.878 -1.026
3 797 848 130 140 667 708 805 836 132 144 675 696 0 0 202 191 30 45 100 100 100 100 1375 1371 .942 1.061 1.031 1.078 1.086 1.253 52 329 1.045 .888 90 2180 6240 99 108 105 114 0 808 133 675 1.012 797 663 .988 .983 .017 -.025
4 985 491 124 148 861 343 1014 483 130 147 890 335 0 0 194 128 32 41 100 100 100 100 1204 1225 2.51 .398 .376 .379 .399 1.373 32 218 .382 .769 70 2320 6230 99 106 120 127 0 468 141 327 .38 460 319 2.634 .359 -1.397 -1.479
5 981 518 131 135 850 383 946 483 135 141 815 348 0 0 212 141 35 43 100 100 100 100 1233 1163 2.219 .451 .427 .433 .435 1.386 52 348 .439 .822 90 2470 6230 98 107 134 143 0 494 129 365 .429 460 332 2.328 .407 -1.219 -1.297
6 570 399 132 142 438 257 571 412 132 145 439 270 0 0 82 88 29 41 100 100 100 96 695 709 1.704 .587 .615 .556 .622 1.503 32 171 .557 .67 60 2620 6230 100 106 151 157 0 380 135 245 .559 393 257 1.788 .586 -.838 -.77
7 677 706 128 143 549 563 673 713 131 144 545 570 0 0 127 127 31 44 100 100 100 100 1112 1115 .975 1.026 1.046 1.027 .967 1.328 52 317 1.008 .815 90 2760 6240 99 108 163 172 0 673 136 537 .977 680 543 1.023 .997 -.033 -.004
8 753 419 126 126 627 293 710 389 127 133 584 263 0 0 182 137 32 43 100 100 100 96 920 847 2.14 .467 .45 .434 .453 1.53 52 312 .451 .757 90 2900 6230 98 107 177 186 0 399 120 279 .445 371 251 2.245 .429 -1.167 -1.22
9 507 540 124 124 383 416 495 536 127 129 371 412 0 0 106 141 32 38 100 100 100 100 799 783 .921 1.086 1.111 1.047 1.084 1.557 52 322 1.152 .773 90 3060 6230 98 107 193 202 0 515 118 397 1.035 511 393 .966 1.059 .05 .082
10 806 775 133 127 673 648 763 772 133 133 630 645 0 0 195 212 33 43 100 100 100 100 1321 1275 1.039 .963 1.024 .944 .999 1.41 52 288 .96 .863 90 3200 6230 98 107 207 216 0 739 121 618 .918 736 615 1.09 .976 -.124 -.035
11 460 424 130 135 330 289 450 423 132 136 320 288 0 0 112 108 32 37 100 98 100 94 619 608 1.142 .876 .9 .853 .898 1.517 52 273 .868 .79 80 3340 6230 99 107 222 230 0 404 129 275 .835 403 275 1.198 .858 -.261 -.221
12 592 612 124 134 468 478 550 594 127 139 426 460 0 0 372 272 31 40 100 100 100 100 946 886 .979 1.021 1.08 1.029 1.024 1.409 52 317 .995 .812 90 3500 6240 99 108 237 246 0 583 128 456 .974 566 438 1.027 1.029 -.039 .042
13 743 848 127 131 616 717 722 838 127 135 595 707 0 0 203 178 31 39 100 100 100 100 1333 1302 .859 1.164 1.188 1.169 1.235 1.423 52 301 1.119 .853 90 3640 6230 98 107 251 260 0 808 125 683 1.109 799 674 .901 1.133 .15 .18
14 705 821 126 132 579 689 724 823 127 132 598 691 0 0 255 317 30 39 98 100 97 98 1268 1289 .84 1.19 1.156 1.222 1.198 1.72 80 381 1.213 .889 100 3790 6230 98 108 266 276 0 783 126 657 1.134 784 659 .882 1.101 .182 .139
15 476 457 124 133 352 324 454 446 127 132 330 313 0 0 125 90 29 36 100 100 100 100 676 643 1.086 .92 .948 .947 .888 1.445 52 276 .881 .8 90 3930 6240 99 108 280 289 0 436 127 309 .877 425 298 1.14 .904 -.189 -.145
16 1385 1734 124 130 1261 1604 1292 1673 127 131 1168 1543 0 0 454 481 30 39 100 100 100 100 2865 2711 .786 1.272 1.321 1.295 1.275 1.204 52 336 1.248 .945 90 4080 6230 98 107 295 304 0 1653 124 1529 1.212 1595 1471 .825 1.259 .278 .333
17 686 477 119 129 567 348 652 456 124 134 533 327 0 0 161 151 30 40 100 100 100 100 915 860 1.629 .614 .614 .582 .596 1.348 52 254 .637 .853 80 4230 6230 99 107 311 319 0 455 123 332 .585 435 312 1.709 .585 -.773 -.774
18 832 953 123 138 709 815 860 923 126 141 737 785 0 0 239 213 30 40 100 100 100 100 1524 1522 .87 1.15 1.065 1.18 1.174 1.228 52 264 1.109 .914 80 4370 6230 99 107 325 333 0 908 132 777 1.096 880 748 .913 1.015 .132 .022
19 1580 1739 127 129 1453 1610 1479 1638 130 133 1352 1509 0 0 417 442 30 39 100 100 100 100 3063 2861 .902 1.108 1.116 1.11 1.11 1.159 52 300 1.092 .929 90 4520 6230 98 107 339 348 0 1658 123 1535 1.056 1561 1438 .947 1.064 .079 .089
20 727 654 126 129 601 525 719 647 131 132 593 518 0 0 143 99 39 37 100 100 100 100 1126 1111 1.145 .874 .874 .884 .825 1.319 52 316 .858 .828 90 4660 6230 98 107 353 362 0 623 123 500 .833 617 494 1.201 .833 -.264 -.264

Total number of rows: 41664

Table truncated, full table size 9461 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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