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Sample GSM148710 Query DataSets for GSM148710
Status Public on Oct 03, 2007
Title PT112_5 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49679.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT112_5 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT112_5 DNA
Prostate genomic DNA; LabeledExtract: 49679.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 = 840, 5080; 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 = 38.38; Parameter Scan Time = 09:31:06; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149962; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; 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 = 38.38; Parameter Scan Time = 09:31:06; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; 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/2004-02/49679.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
1 826 864 165 280 661 584 856 895 169 284 691 615 0 0 188 271 50 75 100 96 100 92 1245 1306 1.132 .884 .89 .794 .906 1.829 52 290 .954 .751 80 1670 5900 78 86 79 87 0 749 243 506 .766 776 533 1.305 .772 -.384 -.374
2 1272 840 160 255 1112 585 1316 787 163 264 1156 532 0 0 185 221 39 60 100 100 100 100 1697 1688 1.901 .526 .46 .5 .543 1.415 32 170 .483 .693 60 1820 5900 79 85 95 101 0 728 221 507 .456 682 461 2.192 .399 -1.132 -1.325
3 1471 1683 149 248 1322 1435 1523 1722 155 252 1374 1474 0 0 404 486 37 54 100 100 100 100 2757 2848 .921 1.085 1.073 1.071 1.085 1.274 52 287 1.11 .907 80 1960 5900 78 86 108 116 0 1459 215 1244 .941 1493 1278 1.062 .93 -.087 -.104
4 1195 623 159 261 1036 362 1226 639 171 271 1067 378 0 0 241 187 63 81 100 93 100 84 1398 1445 2.862 .349 .354 .351 .39 1.916 32 170 .3 .418 60 2110 5900 79 85 124 130 0 540 226 314 .303 554 328 3.301 .307 -1.723 -1.703
5 1776 1027 151 248 1625 779 1617 990 156 248 1466 742 0 0 626 453 35 58 100 100 100 100 2404 2208 2.086 .479 .506 .426 .463 1.536 52 298 .512 .841 80 2250 5900 78 86 137 145 0 890 215 675 .416 858 643 2.406 .439 -1.267 -1.188
6 912 586 152 241 760 345 929 598 156 247 777 357 0 0 157 179 38 62 100 90 100 90 1105 1134 2.203 .454 .459 .377 .429 1.908 32 211 .462 .715 70 2410 5910 79 86 153 160 0 508 209 299 .394 519 310 2.541 .398 -1.345 -1.328
7 1276 1435 149 247 1127 1188 1320 1561 152 246 1171 1314 0 0 314 413 35 54 100 100 100 100 2315 2485 .949 1.054 1.122 1.018 1.109 1.417 52 276 1.092 .886 80 2560 5900 78 86 168 176 0 1244 214 1030 .914 1354 1139 1.094 .973 -.13 -.04
8 1291 1427 152 232 1139 1195 1287 1542 155 238 1135 1310 0 0 267 372 37 54 100 100 100 100 2334 2445 .953 1.049 1.154 1.018 1.085 1.378 52 257 1.078 .905 80 2710 5900 78 86 183 191 0 1237 201 1036 .91 1337 1136 1.099 1.001 -.137 .001
9 771 932 150 243 621 689 783 981 155 245 633 738 0 0 209 276 36 54 100 100 100 100 1310 1371 .901 1.11 1.166 1.079 1.169 1.472 52 254 1.168 .852 80 2850 5900 78 86 197 205 0 808 211 597 .962 851 640 1.039 1.011 -.056 .016
10 1219 1269 153 243 1066 1026 1235 1275 157 247 1082 1032 0 0 270 301 36 50 100 100 100 100 2092 2114 1.039 .962 .954 .949 1.003 1.37 52 267 .975 .881 80 3000 5900 78 86 212 220 0 1100 211 890 .835 1106 895 1.198 .827 -.261 -.274
11 836 952 147 244 689 708 808 998 160 248 661 754 0 0 199 181 58 53 100 100 100 100 1397 1415 .973 1.028 1.141 1.037 1.113 1.37 32 220 .982 .768 70 3140 5890 77 84 226 233 0 825 212 614 .891 865 654 1.122 .989 -.167 -.016
12 1184 1009 162 251 1022 758 1223 1005 169 257 1061 754 0 0 221 155 72 60 100 100 100 100 1780 1815 1.348 .742 .711 .748 .724 1.262 32 232 .694 .837 70 3280 5890 77 84 240 247 0 875 218 657 .643 871 654 1.555 .616 -.637 -.699
13 1044 1319 150 249 894 1070 1075 1418 154 254 925 1169 0 0 213 336 37 58 100 100 100 100 1964 2094 .836 1.197 1.264 1.162 1.235 1.491 52 283 1.247 .834 80 3440 5900 78 86 256 264 0 1144 216 928 1.038 1230 1014 .964 1.096 .054 .132
14 1206 1461 148 240 1058 1221 1182 1518 152 244 1034 1278 0 0 165 243 35 53 100 100 100 100 2279 2312 .867 1.154 1.236 1.142 1.151 1.315 52 277 1.174 .831 80 3590 5900 78 86 271 279 0 1267 208 1059 1.001 1316 1108 .999 1.072 .001 .1
15 767 848 151 240 616 608 786 865 154 244 635 625 0 0 152 182 35 56 100 100 100 100 1224 1260 1.013 .987 .984 .97 1.023 1.423 52 264 1.027 .763 80 3740 5900 78 86 286 294 0 735 208 527 .856 750 542 1.168 .853 -.225 -.229
16 2115 2848 155 241 1960 2607 2127 3124 158 244 1972 2883 0 0 839 1124 44 57 100 100 100 100 4567 4855 .752 1.33 1.462 1.337 1.459 1.523 52 270 1.348 .885 80 3890 5900 78 86 301 309 0 2469 209 2260 1.153 2709 2500 .867 1.268 .206 .342
17 1029 1409 163 246 866 1163 1025 1440 175 251 862 1194 0 0 258 298 82 65 100 100 100 100 2029 2056 .745 1.343 1.385 1.368 1.325 1.35 32 200 1.228 .829 70 4020 5890 77 84 314 321 0 1222 213 1008 1.164 1249 1035 .859 1.201 .22 .264
18 1206 1436 151 248 1055 1188 1301 1554 158 251 1150 1306 0 0 320 396 57 55 100 100 98 100 2243 2456 .888 1.126 1.136 1.133 1.15 1.436 52 277 1.138 .875 80 4160 5900 78 86 328 336 0 1245 215 1030 .976 1347 1132 1.024 .985 -.034 -.022
19 2569 2981 147 241 2422 2740 2666 3124 152 249 2519 2883 0 0 824 834 42 59 100 100 100 100 5162 5402 .884 1.131 1.145 1.178 1.155 1.374 52 313 1.084 .887 90 4310 5900 77 86 342 351 0 2585 209 2376 .981 2709 2500 1.019 .992 -.028 -.011
20 1087 1075 153 235 934 840 1077 1066 157 244 924 831 0 0 220 242 43 60 100 100 100 100 1774 1755 1.112 .899 .899 .889 .873 1.317 52 285 .895 .783 80 4460 5900 78 86 358 366 0 932 204 728 .78 924 721 1.282 .78 -.359 -.359

Total number of rows: 41664

Table truncated, full table size 9558 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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