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Sample GSM148697 Query DataSets for GSM148697
Status Public on Oct 03, 2007
Title PT41_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 53659.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT41_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT41_2 DNA
Prostate genomic DNA; LabeledExtract: 53659.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 = 1200, 5880; 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 = 38.86; Parameter Scan Time = 09:51:35; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-10; Parameter Pixel Size = 10; Parameter Laser on time = 174158; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; 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 = 38.86; Parameter Scan Time = 09:51:35; Parameter PMT Volts = 730; Parameter Scan Date = 2004-07-10; Parameter Pixel Size = 10; Parameter Laser on time = 538962; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; 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/2004-07/53659.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
1 516 283 164 183 352 100 512 266 166 189 348 83 0 0 105 106 39 70 100 53 100 30 452 431 3.52 .284 .239 .237 .322 2.951 52 276 .339 .239 80 1690 6460 54 62 45 53 0 297 192 105 .298 279 87 3.355 .25 -1.746 -1.999
2 653 482 169 188 484 294 650 495 171 195 481 307 0 0 141 129 38 71 100 96 100 84 778 788 1.646 .607 .638 .55 .653 1.726 52 317 .624 .592 90 1830 6450 52 61 58 67 0 506 197 308 .637 519 322 1.569 .67 -.65 -.579
3 538 409 171 193 367 216 522 386 171 196 351 193 0 0 82 146 40 69 100 87 100 62 583 544 1.699 .589 .55 .482 .494 2.122 32 220 .662 .435 70 1970 6450 53 60 73 80 0 429 202 227 .617 405 202 1.62 .577 -.696 -.794
4 516 386 175 184 341 202 493 368 179 194 318 184 0 0 112 120 58 77 100 84 100 59 543 502 1.688 .592 .579 .523 .532 1.813 32 226 .603 .517 70 2120 6450 53 60 88 95 0 405 193 212 .621 386 193 1.609 .607 -.686 -.72
5 410 292 167 182 243 110 401 279 171 194 234 97 0 0 78 86 39 71 100 65 100 26 353 331 2.209 .453 .415 .378 .433 2.626 52 329 .798 .268 90 2270 6460 53 62 102 111 0 306 191 115 .475 293 102 2.106 .435 -1.074 -1.201
6 474 340 165 180 309 160 506 329 170 195 341 149 0 0 110 130 40 70 96 71 96 56 469 490 1.931 .518 .437 .462 .451 1.884 32 219 .611 .352 70 2410 6450 53 60 117 124 0 357 189 168 .543 345 156 1.841 .458 -.88 -1.125
7 492 281 165 173 327 108 495 270 168 179 330 97 0 0 89 74 38 64 100 75 100 28 435 427 3.028 .33 .294 .303 .349 2.186 32 224 .294 .22 70 2560 6450 53 60 132 139 0 295 181 113 .346 283 102 2.886 .308 -1.529 -1.697
8 577 381 166 170 411 211 581 350 170 183 415 180 0 0 145 120 42 69 100 94 100 73 622 595 1.948 .513 .434 .482 .509 1.883 52 252 .502 .501 80 2710 6450 53 61 147 155 0 400 178 221 .539 367 189 1.857 .455 -.893 -1.136
9 554 502 166 190 388 312 542 485 171 197 376 295 0 0 96 114 41 68 100 98 100 93 700 671 1.244 .804 .785 .768 .819 1.633 80 319 .823 .647 100 2850 6450 52 62 160 170 0 527 199 327 .844 509 309 1.185 .823 -.245 -.281
10 971 858 172 188 799 670 991 856 172 197 819 668 0 0 171 184 41 67 100 100 100 100 1469 1487 1.193 .839 .816 .825 .807 1.289 80 348 .833 .85 110 2990 6450 51 62 173 184 0 900 197 703 .88 898 701 1.137 .856 -.185 -.225
11 427 430 167 191 260 239 424 427 170 199 257 236 0 0 92 104 41 67 98 96 96 83 499 493 1.088 .919 .918 .914 .94 1.751 80 332 .984 .538 100 3140 6460 53 63 189 199 0 451 200 251 .964 448 248 1.037 .963 -.052 -.054
12 624 650 172 194 452 456 614 631 173 200 442 437 0 0 100 160 42 67 100 100 100 100 908 879 .991 1.009 .989 .976 .965 1.488 52 289 1.06 .717 90 3280 6450 52 61 203 212 0 682 204 478 1.058 662 458 .945 1.037 .082 .053
13 635 698 171 184 464 514 621 692 174 188 450 508 0 0 101 182 43 67 100 98 100 96 978 958 .903 1.108 1.129 1.034 1.079 1.649 80 357 1.185 .748 100 3430 6450 52 62 218 228 0 732 193 539 1.162 726 533 .86 1.184 .217 .244
14 770 849 169 186 601 663 757 839 172 195 588 653 0 0 119 206 39 69 100 100 100 100 1264 1241 .906 1.103 1.111 1.071 1.07 1.415 80 354 1.165 .779 100 3580 6450 52 62 233 243 0 891 195 696 1.157 880 685 .864 1.165 .211 .22
15 478 477 165 195 313 282 460 476 167 202 295 281 0 0 119 125 38 70 100 96 98 87 595 576 1.11 .901 .953 .853 .906 1.983 80 385 .939 .61 110 3720 6450 51 62 246 257 0 500 205 296 .945 499 295 1.058 .999 -.081 -.001
16 1976 2324 163 202 1813 2122 1897 2245 168 206 1734 2043 0 0 512 559 49 70 100 100 100 100 3935 3777 .854 1.17 1.178 1.179 1.173 1.236 80 350 1.167 .936 100 3870 6450 52 62 262 272 0 2438 212 2226 1.228 2355 2143 .814 1.236 .296 .306
17 849 979 166 197 683 782 884 990 170 205 718 793 0 0 160 207 41 67 100 100 100 100 1465 1511 .873 1.145 1.104 1.142 1.13 1.368 80 338 1.162 .856 100 4020 6450 52 62 277 287 0 1027 207 820 1.201 1039 832 .833 1.159 .264 .212
18 900 949 168 190 732 759 913 975 174 195 745 785 0 0 170 217 41 61 100 100 100 100 1491 1530 .964 1.037 1.054 1.018 1.001 1.393 80 324 1.071 .829 100 4170 6450 52 62 292 302 0 996 199 796 1.088 1023 824 .919 1.105 .121 .145
19 1952 1675 166 188 1786 1487 1962 1655 168 194 1796 1467 0 0 445 474 37 64 100 100 100 100 3273 3263 1.201 .833 .817 .816 .829 1.251 80 359 .843 .895 110 4310 6450 51 62 305 316 0 1757 197 1560 .873 1736 1539 1.145 .857 -.195 -.223
20 752 591 166 191 586 400 762 573 168 197 596 382 0 0 137 136 40 64 100 100 100 97 986 978 1.465 .683 .641 .658 .676 1.547 80 382 .695 .72 110 4450 6450 51 62 319 330 0 620 200 420 .716 601 401 1.396 .672 -.482 -.573

Total number of rows: 41472

Table truncated, full table size 9461 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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