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Sample GSM148726 Query DataSets for GSM148726
Status Public on Oct 03, 2007
Title PT191_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52832.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT191_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT191_1 DNA
Prostate genomic DNA; LabeledExtract: 52832.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 = 38.82; Parameter Scan Time = 10:33:40; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167400; 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 = 38.82; Parameter Scan Time = 10:33:40; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532303; 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/2004-06/52832.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
1 425 289 171 170 254 119 426 282 176 175 255 112 0 0 95 79 43 50 96 82 96 55 373 367 2.134 .469 .439 .444 .523 2.113 52 344 .474 .353 90 1860 6460 93 102 53 62 0 227 133 93 .367 221 88 2.722 .344 -1.445 -1.538
2 668 551 166 170 502 381 661 582 171 178 495 412 0 0 192 163 44 54 98 100 98 92 883 907 1.318 .759 .832 .754 .739 1.689 52 275 .74 .83 80 2000 6460 94 102 68 76 0 432 133 299 .595 456 323 1.68 .653 -.749 -.616
3 424 427 165 172 259 255 429 416 172 179 264 244 0 0 71 89 44 49 100 100 100 100 514 508 1.016 .985 .924 .968 .975 1.403 32 215 .971 .628 70 2150 6470 95 102 83 90 0 335 135 200 .772 326 191 1.295 .725 -.373 -.464
4 472 433 171 180 301 253 460 415 187 191 289 235 0 0 111 127 82 63 100 100 93 90 554 524 1.19 .841 .813 .799 .797 1.592 32 220 .715 .557 70 2290 6460 94 101 97 104 0 340 141 198 .659 325 184 1.517 .638 -.601 -.649
5 386 390 177 172 209 218 390 379 192 184 213 207 0 0 59 77 79 74 98 100 80 88 427 420 .959 1.043 .972 1.023 1.015 1.517 52 294 1.073 .522 80 2440 6460 94 102 112 120 0 306 135 171 .818 297 162 1.223 .762 -.29 -.392
6 439 359 172 178 267 181 449 339 181 188 277 161 0 0 68 88 69 72 100 90 96 65 448 438 1.475 .678 .581 .622 .666 1.66 32 221 .648 .493 70 2590 6460 94 101 127 134 0 282 140 142 .532 266 126 1.881 .456 -.912 -1.134
7 460 391 168 177 292 214 470 377 175 182 302 200 0 0 71 84 60 51 100 100 96 90 506 502 1.364 .733 .662 .7 .719 1.664 32 222 .741 .595 70 2730 6460 94 101 141 148 0 307 139 168 .575 296 157 1.74 .519 -.799 -.945
8 542 481 166 171 376 310 503 482 185 178 337 311 0 0 158 145 127 67 100 96 78 90 686 648 1.213 .824 .923 .796 .798 1.561 32 214 .791 .676 70 2870 6460 94 101 155 162 0 377 134 243 .647 378 244 1.547 .724 -.629 -.467
9 466 679 163 172 303 507 456 672 168 176 293 500 0 0 76 103 43 45 100 100 100 100 810 793 .598 1.673 1.706 1.693 1.638 1.323 52 312 1.582 .656 90 3020 6460 93 102 169 178 0 532 135 398 1.312 527 392 .762 1.338 .392 .42
10 688 857 169 171 519 686 657 877 174 174 488 706 0 0 199 264 48 55 100 100 100 97 1205 1194 .757 1.322 1.447 1.28 1.34 1.45 80 355 1.333 .84 100 3170 6460 93 103 184 194 0 672 134 538 1.036 688 554 .965 1.134 .052 .182
11 567 606 164 170 403 436 450 494 169 173 286 324 0 0 477 343 43 63 100 100 100 100 839 610 .924 1.082 1.133 1.182 1.11 1.364 52 288 .867 .842 90 3310 6460 93 102 198 207 0 475 133 342 .848 387 254 1.179 .888 -.237 -.171
12 588 809 163 173 425 636 570 799 167 175 407 626 0 0 98 135 38 44 100 100 100 100 1061 1033 .668 1.496 1.538 1.499 1.504 1.334 52 312 1.515 .823 90 3460 6460 93 102 213 222 0 634 136 499 1.173 627 491 .852 1.206 .231 .27
13 729 984 165 167 564 817 646 953 168 170 481 786 0 0 554 303 36 42 100 100 100 100 1381 1267 .69 1.449 1.634 1.583 1.611 1.292 52 300 1.08 .75 90 3600 6460 93 102 227 236 0 772 131 641 1.136 747 616 .88 1.281 .184 .358
14 770 963 164 162 606 801 751 976 167 165 587 814 0 0 175 231 47 47 100 100 98 100 1407 1401 .757 1.322 1.387 1.325 1.348 1.438 80 368 1.342 .883 100 3750 6460 93 103 242 252 0 755 127 628 1.036 765 638 .965 1.087 .052 .121
15 441 545 162 169 279 376 424 521 165 170 262 352 0 0 123 141 42 44 100 100 97 100 655 614 .742 1.348 1.344 1.362 1.341 1.462 80 313 1.335 .806 100 3900 6460 93 103 257 267 0 427 133 295 1.057 409 276 .946 1.054 .08 .075
16 1612 2833 158 164 1454 2669 1704 3169 160 164 1546 3005 0 0 641 1036 33 42 97 100 97 100 4123 4551 .545 1.836 1.944 1.987 1.865 1.624 80 340 1.82 .946 100 4040 6460 93 103 271 281 0 2221 129 2093 1.439 2485 2356 .695 1.524 .525 .608
17 717 1018 153 162 564 856 690 1005 159 167 537 843 0 0 129 162 40 48 100 100 100 100 1420 1380 .659 1.518 1.57 1.53 1.574 1.253 52 277 1.5 .881 90 4190 6460 93 102 286 295 0 798 127 671 1.19 788 661 .84 1.231 .251 .3
18 812 1181 157 167 655 1014 810 1192 164 174 653 1025 0 0 141 203 42 47 100 100 100 100 1669 1678 .646 1.548 1.57 1.549 1.523 1.209 52 313 1.525 .897 90 4330 6450 92 101 300 309 0 926 131 795 1.214 935 804 .824 1.231 .28 .3
19 1531 2337 159 174 1372 2163 1495 2282 169 185 1336 2108 0 0 309 403 78 96 100 100 100 100 3535 3444 .634 1.577 1.578 1.587 1.572 1.164 52 324 1.55 .935 90 4480 6450 92 101 315 324 0 1833 136 1696 1.236 1789 1653 .809 1.237 .306 .307
20 649 736 159 174 490 562 624 721 171 185 465 547 0 0 170 166 77 94 100 100 100 100 1052 1012 .872 1.147 1.176 1.154 1.165 1.316 52 325 1.179 .856 90 4630 6450 92 101 330 339 0 577 136 441 .899 565 429 1.112 .922 -.153 -.116

Total number of rows: 41472

Table truncated, full table size 9472 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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