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Sample GSM148723 Query DataSets for GSM148723
Status Public on Oct 03, 2007
Title PT187_3 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52830.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT187_3 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT187_3 DNA
Prostate genomic DNA; LabeledExtract: 52830.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 = 38.69; Parameter Scan Time = 10:07:25; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167374; 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 = 38.69; Parameter Scan Time = 10:07:25; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532278; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; 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/2004-06/52830.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
1 650 578 183 180 467 398 645 572 195 183 462 392 0 0 99 106 70 50 100 100 100 100 865 854 1.173 .852 .848 .836 .858 1.367 32 224 .757 .838 70 1750 6230 71 78 43 50 0 466 145 321 .687 461 316 1.456 .684 -.542 -.548
2 939 1013 187 188 752 825 981 1065 203 207 794 877 0 0 368 395 124 121 96 100 92 90 1577 1671 .912 1.097 1.105 1.112 1.04 1.607 52 274 1.077 .839 80 1900 6230 71 79 58 66 0 817 152 665 .884 858 707 1.131 .89 -.177 -.168
3 530 634 191 186 339 448 549 672 196 196 358 486 0 0 169 209 56 82 96 96 86 84 787 844 .757 1.322 1.358 1.3 1.327 1.601 52 272 1.319 .806 80 2040 6230 71 79 72 80 0 511 150 361 1.065 542 392 .939 1.094 .091 .13
4 617 697 198 205 419 492 620 674 219 222 422 469 0 0 181 223 124 121 90 96 88 86 911 891 .852 1.174 1.111 1.222 1.168 1.852 52 260 1.164 .772 80 2200 6230 71 79 88 96 0 562 165 397 .947 543 378 1.056 .896 -.079 -.159
5 604 666 198 207 406 459 601 665 210 229 403 458 0 0 120 143 91 116 100 98 98 96 865 861 .885 1.131 1.136 1.112 1.195 1.432 52 288 1.177 .746 90 2330 6230 70 79 100 109 0 537 167 370 .911 536 369 1.097 .916 -.134 -.126
6 565 612 193 202 372 410 557 628 207 215 364 426 0 0 130 158 99 106 96 96 87 93 782 790 .907 1.102 1.17 1.033 1.169 1.912 32 171 1.003 .77 60 2480 6230 72 78 117 123 0 493 163 330 .888 506 343 1.126 .943 -.171 -.084
7 565 602 192 192 373 410 531 524 195 197 339 332 0 0 227 222 50 48 96 100 93 96 783 671 .91 1.099 .979 1.157 .979 1.916 32 220 .468 .302 70 2620 6240 72 79 130 137 0 485 155 330 .886 422 268 1.129 .789 -.175 -.341
8 677 755 194 194 483 561 666 727 197 200 472 533 0 0 254 289 48 44 96 100 96 98 1044 1005 .861 1.161 1.129 1.235 1.139 1.646 52 260 .761 .608 80 2780 6230 71 79 146 154 0 609 156 452 .936 586 430 1.068 .91 -.095 -.136
9 650 979 188 193 462 786 677 983 190 198 489 790 0 0 184 299 43 47 100 100 97 98 1248 1279 .588 1.701 1.616 1.732 1.641 1.571 80 341 1.768 .822 100 2920 6230 70 80 159 169 0 789 156 634 1.371 792 637 .729 1.302 .456 .381
10 1090 1466 191 201 899 1265 1149 1575 199 211 958 1374 0 0 376 425 79 87 100 100 95 98 2164 2332 .711 1.407 1.434 1.483 1.399 1.42 80 343 1.367 .914 100 3070 6230 70 80 174 184 0 1182 162 1020 1.134 1270 1108 .882 1.156 .182 .209
11 728 840 191 200 537 640 667 824 201 211 476 624 0 0 261 164 82 93 100 100 100 100 1177 1100 .839 1.192 1.311 1.242 1.23 1.292 52 289 1.09 .815 90 3210 6230 70 79 188 197 0 677 161 516 .961 664 503 1.041 1.057 -.058 .08
12 870 1163 179 196 691 967 917 1191 188 204 738 995 0 0 191 170 53 71 100 100 98 100 1658 1733 .715 1.399 1.348 1.467 1.402 1.422 52 302 1.371 .845 90 3350 6220 69 78 202 211 0 937 158 779 1.128 960 802 .886 1.087 .174 .12
13 876 1246 184 194 692 1052 919 1341 186 199 735 1147 0 0 285 324 39 47 97 100 96 100 1744 1882 .658 1.52 1.561 1.637 1.528 1.67 80 357 1.467 .895 100 3500 6230 70 80 217 227 0 1004 156 848 1.225 1081 925 .816 1.258 .293 .331
14 1080 1426 187 201 893 1225 1126 1440 192 200 939 1239 0 0 278 297 49 46 100 100 100 100 2118 2178 .729 1.372 1.319 1.421 1.355 1.383 80 345 1.349 .912 100 3650 6230 70 80 232 242 0 1149 162 987 1.106 1161 999 .904 1.064 .145 .089
15 641 824 190 200 451 624 637 840 196 201 447 640 0 0 109 105 55 46 100 100 100 100 1075 1087 .723 1.384 1.432 1.401 1.426 1.262 52 263 1.391 .843 90 3780 6230 70 79 245 254 0 664 161 503 1.115 677 516 .897 1.154 .157 .207
16 2547 4391 183 202 2364 4189 2753 4748 187 205 2570 4546 0 0 1060 1449 43 47 100 100 98 100 6553 7116 .564 1.772 1.769 1.979 1.779 1.627 80 352 1.707 .954 100 3940 6230 70 80 261 271 0 3540 163 3377 1.428 3827 3665 .7 1.426 .514 .512
17 912 1239 183 195 729 1044 890 1198 185 202 707 1003 0 0 181 230 41 53 100 100 100 100 1773 1710 .698 1.432 1.419 1.444 1.417 1.266 52 288 1.421 .878 90 4080 6220 69 78 275 284 0 999 157 842 1.154 966 809 .866 1.144 .207 .194
18 1310 1635 185 205 1125 1430 1336 1655 189 211 1151 1450 0 0 247 282 41 52 100 100 100 100 2555 2601 .787 1.271 1.26 1.276 1.263 1.204 52 313 1.273 .921 90 4230 6220 69 78 290 299 0 1318 165 1153 1.025 1334 1169 .976 1.015 .035 .022
19 2006 2924 180 204 1826 2720 2187 3037 182 207 2007 2833 0 0 708 861 38 49 100 100 100 100 4546 4840 .671 1.49 1.412 1.577 1.466 1.438 80 350 1.453 .941 100 4380 6230 70 80 305 315 0 2357 164 2193 1.201 2448 2284 .833 1.138 .264 .186
20 928 1088 182 203 746 885 946 1116 186 207 764 913 0 0 211 173 42 54 100 100 100 100 1631 1677 .843 1.186 1.195 1.226 1.173 1.32 52 276 1.164 .891 90 4510 6220 69 78 318 327 0 877 164 713 .956 900 736 1.046 .963 -.064 -.054

Total number of rows: 41472

Table truncated, full table size 9532 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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