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Sample GSM148699 Query DataSets for GSM148699
Status Public on Oct 03, 2007
Title PT319_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48001.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT319_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT319_2 DNA
Prostate genomic DNA; LabeledExtract: 48001.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 = 800, 4960; 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 = 38.56; Parameter Scan Time = 11:38:04; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142641; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; 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 = 38.56; Parameter Scan Time = 11:38:04; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507707; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.17; 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/2004-01/48001.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
1 758 645 141 166 617 479 785 685 143 171 644 519 0 0 211 215 32 45 100 100 100 96 1096 1163 1.288 .776 .806 .729 .741 1.528 52 299 .815 .859 80 1760 6500 150 158 92 100 0 557 143 414 .671 592 448 1.491 .696 -.577 -.523
2 1391 852 144 177 1247 675 1432 867 148 177 1288 690 0 0 328 277 37 44 100 100 100 100 1922 1978 1.847 .541 .536 .506 .538 1.451 32 218 .531 .842 70 1910 6500 150 157 107 114 0 736 153 583 .468 749 596 2.139 .463 -1.097 -1.112
3 1360 1492 146 172 1214 1320 1425 1538 147 175 1279 1366 0 0 470 462 35 40 100 100 98 100 2534 2645 .92 1.087 1.068 1.167 1.089 1.641 52 335 1.069 .932 90 2050 6510 150 159 120 129 0 1289 149 1140 .939 1328 1180 1.065 .923 -.091 -.116
4 1195 602 144 165 1051 437 1278 632 145 169 1134 467 0 0 348 194 34 43 100 100 100 96 1488 1601 2.405 .416 .412 .393 .421 1.438 32 211 .403 .846 70 2200 6500 150 157 136 143 0 520 143 377 .359 546 403 2.784 .356 -1.477 -1.491
5 1548 1427 141 166 1407 1261 1545 1439 144 169 1404 1273 0 0 505 475 49 44 100 100 100 100 2668 2677 1.116 .896 .907 .906 .861 1.402 52 270 .895 .914 80 2330 6510 151 159 149 157 0 1233 143 1089 .774 1243 1100 1.292 .783 -.369 -.353
6 1060 777 142 172 918 605 1100 811 145 174 958 639 0 0 299 226 35 43 100 100 100 100 1523 1597 1.517 .659 .667 .672 .669 1.606 32 218 .613 .777 70 2490 6510 151 158 165 172 0 671 149 523 .569 701 552 1.757 .576 -.813 -.795
7 1240 1365 141 184 1099 1181 1269 1385 144 183 1128 1201 0 0 295 236 34 44 100 100 100 100 2280 2329 .931 1.075 1.065 1.101 1.061 1.255 52 258 1.06 .925 80 2640 6510 151 159 180 188 0 1179 159 1020 .928 1196 1037 1.077 .92 -.107 -.121
8 1201 1259 144 178 1057 1081 1279 1302 147 182 1135 1124 0 0 378 318 36 41 100 100 100 100 2138 2259 .978 1.023 .99 1.093 1.013 1.533 52 243 .979 .919 80 2780 6510 151 159 194 202 0 1087 154 934 .883 1125 971 1.132 .855 -.179 -.225
9 909 1023 145 181 764 842 903 1062 147 187 758 881 0 0 218 278 34 43 100 100 100 100 1606 1639 .907 1.102 1.162 1.086 1.1 1.275 52 254 1.134 .89 80 2930 6500 150 158 209 217 0 884 156 727 .952 917 761 1.05 1.004 -.071 .006
10 1636 1440 149 180 1487 1260 1666 1534 152 184 1517 1354 0 0 311 275 34 47 100 100 100 100 2747 2871 1.18 .847 .893 .844 .844 1.157 52 300 .837 .929 90 3070 6500 149 158 222 231 0 1244 155 1088 .732 1325 1170 1.366 .771 -.45 -.375
11 816 817 147 175 669 642 857 850 147 181 710 675 0 0 212 231 34 44 100 100 100 100 1311 1385 1.042 .96 .951 .932 1.016 1.52 52 324 .977 .863 90 3220 6500 149 158 237 246 0 706 151 555 .829 734 583 1.206 .821 -.271 -.284
12 1055 1098 146 177 909 921 1125 1200 149 180 979 1023 0 0 277 293 32 42 100 100 100 98 1830 2002 .987 1.013 1.045 1.002 1.014 1.332 52 276 1.021 .918 80 3370 6500 150 158 253 261 0 948 153 796 .875 1037 884 1.143 .903 -.192 -.148
13 1295 1637 144 182 1151 1455 1241 1703 458 188 1097 1521 0 0 236 384 3536 63 0 100 0 100 2606 2618 .791 1.264 1.387 1.238 1.285 1.252 52 300 .021 .016 90 3520 6500 149 158 267 276 0 1414 157 1257 1.092 1471 1314 .916 1.198 .127 .26
14 1615 2048 145 191 1470 1857 1632 2096 154 194 1487 1905 0 0 251 313 61 49 100 100 100 100 3327 3392 .792 1.263 1.281 1.264 1.259 1.198 52 325 1.289 .892 90 3660 6500 149 158 281 290 0 1769 165 1604 1.091 1810 1645 .916 1.107 .126 .146
15 844 965 150 185 694 780 843 997 151 189 693 812 0 0 153 194 36 44 100 100 100 100 1474 1505 .89 1.124 1.172 1.114 1.132 1.376 52 272 1.123 .853 80 3810 6500 150 158 297 305 0 834 160 674 .971 861 701 1.03 1.012 -.043 .017
16 3591 4755 149 183 3442 4572 3839 5002 166 193 3690 4819 0 0 1425 1946 180 70 100 100 100 100 8014 8509 .753 1.328 1.306 1.311 1.309 1.294 52 328 1.351 .939 90 3970 6500 149 158 312 321 0 4107 158 3949 1.147 4321 4163 .872 1.128 .198 .174
17 1320 1580 145 180 1175 1400 1419 1736 149 185 1274 1556 0 0 470 513 34 42 98 100 98 100 2575 2830 .839 1.191 1.221 1.284 1.259 1.749 52 223 1.17 .912 80 4110 6510 151 159 327 335 0 1365 155 1209 1.029 1500 1344 .972 1.055 .041 .077
18 1652 2016 145 176 1507 1840 1688 1986 150 183 1543 1810 0 0 346 460 36 43 100 100 100 100 3347 3353 .819 1.221 1.173 1.214 1.224 1.24 52 290 1.231 .919 90 4250 6500 149 158 340 349 0 1741 152 1589 1.055 1715 1563 .948 1.013 .077 .019
19 4058 3578 145 183 3913 3395 2750 2699 150 189 2605 2516 0 0 3701 2754 38 47 100 100 100 100 7308 5121 1.153 .868 .966 .895 .887 1.267 52 288 .796 .887 90 4390 6500 149 158 354 363 0 3091 158 2933 .749 2331 2173 1.334 .834 -.416 -.261
20 1312 1243 148 189 1164 1054 1293 1224 151 194 1145 1035 0 0 235 204 36 47 100 100 100 100 2218 2180 1.104 .905 .904 .907 .913 1.173 52 326 .891 .902 90 4530 6500 149 158 368 377 0 1074 163 910 .782 1057 894 1.279 .781 -.354 -.357

Total number of rows: 41664

Table truncated, full table size 9778 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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