NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148744 Query DataSets for GSM148744
Status Public on Oct 03, 2007
Title PT130_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47156.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT130_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT130_1 DNA
Prostate genomic DNA; LabeledExtract: 47156.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 = 880, 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 = 38.74; Parameter Scan Time = 11:40:36; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134271; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; 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 = 38.74; Parameter Scan Time = 11:40:36; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499336; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.13; 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/2003-11/47156.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 1052 860 153 182 899 678 1058 904 160 185 905 722 0 0 154 182 68 47 100 100 100 100 1577 1627 1.326 .754 .798 .733 .789 1.297 52 332 .78 .891 90 1770 6070 94 103 84 93 0 912 193 719 .8 959 766 1.25 .846 -.322 -.241
2 1589 901 148 174 1441 727 1690 943 149 179 1542 769 0 0 377 249 33 39 100 100 100 100 2168 2311 1.982 .505 .499 .492 .501 1.28 52 290 .502 .913 90 1900 6070 94 103 97 106 0 956 185 771 .535 1000 816 1.869 .529 -.902 -.919
3 1648 1679 149 178 1499 1501 1760 1808 151 179 1611 1630 0 0 514 512 35 42 100 100 100 100 3000 3241 .999 1.001 1.012 .995 1.02 1.454 80 365 .997 .923 100 2050 6080 95 105 112 122 0 1781 189 1592 1.062 1917 1729 .942 1.073 .087 .102
4 1206 640 149 184 1057 456 1247 643 156 189 1098 459 0 0 285 174 35 41 100 100 100 98 1513 1557 2.318 .431 .418 .413 .409 1.382 52 232 .421 .852 80 2200 6080 96 104 128 136 0 679 195 484 .458 682 487 2.186 .443 -1.128 -1.173
5 1755 812 153 183 1602 629 1605 761 159 189 1452 578 0 0 561 244 38 47 100 100 100 100 2231 2030 2.547 .393 .398 .387 .387 1.232 80 341 .383 .909 100 2340 6080 95 105 141 151 0 861 194 667 .416 807 613 2.401 .422 -1.264 -1.244
6 1073 684 153 183 920 501 1108 701 154 187 955 518 0 0 208 175 33 44 100 100 100 96 1421 1473 1.836 .545 .542 .511 .562 1.52 52 232 .551 .841 80 2490 6080 96 104 157 165 0 725 194 531 .578 743 549 1.731 .575 -.792 -.798
7 1251 1348 151 187 1100 1161 1363 1370 156 187 1212 1183 0 0 428 383 36 41 100 100 98 100 2261 2395 .947 1.055 .976 1.143 1.053 1.613 80 325 1.026 .921 100 2630 6080 95 105 170 180 0 1430 198 1231 1.119 1453 1255 .893 1.035 .163 .05
8 1257 1156 154 185 1103 971 1306 1203 158 188 1152 1018 0 0 295 284 38 42 100 100 100 100 2074 2170 1.136 .88 .884 .869 .889 1.345 80 318 .881 .915 100 2780 6080 95 105 185 195 0 1226 196 1030 .934 1276 1080 1.071 .937 -.099 -.094
9 1009 1024 158 187 851 837 1027 1016 163 191 869 829 0 0 161 175 43 43 100 100 100 100 1688 1698 1.017 .984 .954 .981 1.013 1.227 52 290 .999 .894 90 2920 6070 94 103 199 208 0 1086 198 888 1.043 1078 879 .959 1.012 .061 .017
10 1473 1240 162 194 1311 1046 1546 1289 168 197 1384 1095 0 0 336 291 42 43 100 100 100 100 2357 2479 1.253 .798 .791 .789 .799 1.406 80 341 .797 .906 100 3080 6080 95 105 215 225 0 1315 206 1109 .846 1367 1161 1.182 .839 -.241 -.253
11 975 877 165 188 810 689 968 875 165 193 803 687 0 0 155 125 39 47 100 100 100 100 1499 1490 1.176 .851 .856 .851 .861 1.179 52 288 .859 .873 90 3220 6070 94 103 229 238 0 930 199 731 .902 928 729 1.108 .907 -.149 -.14
12 1107 1017 155 188 952 829 1148 1029 158 189 993 841 0 0 181 182 36 44 100 100 100 100 1781 1834 1.148 .871 .847 .865 .871 1.209 52 300 .865 .9 90 3360 6070 94 103 243 252 0 1079 199 879 .924 1091 892 1.083 .898 -.115 -.155
13 1067 1212 151 192 916 1020 1175 1249 155 193 1024 1057 0 0 317 341 36 45 100 100 100 98 1936 2081 .898 1.114 1.032 1.121 1.095 1.389 80 354 1.117 .922 100 3510 6070 94 104 258 268 0 1285 204 1082 1.181 1325 1121 .847 1.095 .24 .131
14 1245 1219 159 192 1086 1027 1290 1262 163 191 1131 1070 0 0 294 290 36 45 100 100 100 100 2113 2201 1.057 .946 .946 .945 .949 1.311 80 346 .952 .914 100 3660 6070 94 104 273 283 0 1293 204 1089 1.003 1338 1135 .997 1.003 .004 .005
15 711 726 156 192 555 534 709 724 158 194 553 532 0 0 120 121 35 43 100 100 100 100 1089 1085 1.039 .962 .962 .961 .952 1.347 52 289 .955 .824 90 3800 6070 94 103 287 296 0 770 204 566 1.02 768 564 .98 1.02 .029 .029
16 2855 3486 159 189 2696 3297 2977 3583 160 194 2818 3394 0 0 754 731 37 45 100 100 100 100 5993 6212 .818 1.223 1.204 1.244 1.204 1.211 52 312 1.197 .94 90 3950 6070 94 103 302 311 0 3697 200 3497 1.297 3800 3600 .771 1.277 .375 .353
17 1176 1207 154 185 1022 1022 1156 1213 157 188 1002 1028 0 0 268 250 34 45 100 100 100 100 2044 2030 1 1 1.026 1 1.033 1.202 52 300 .997 .918 90 4100 6070 94 103 317 326 0 1280 196 1084 1.061 1286 1090 .943 1.088 .085 .122
18 1136 1034 157 181 979 853 1179 1115 161 186 1022 934 0 0 312 283 33 43 100 100 100 100 1832 1956 1.148 .871 .914 .871 .857 1.347 80 337 .866 .911 100 4250 6070 94 104 332 342 0 1097 192 905 .924 1183 991 1.082 .969 -.114 -.045
19 2708 2635 157 184 2551 2451 2649 2427 160 189 2492 2243 0 0 1019 945 31 44 100 100 100 100 5002 4735 1.041 .961 .9 .988 .94 1.409 80 342 .944 .93 100 4390 6070 94 104 346 356 0 2795 195 2599 1.019 2574 2379 .981 .955 .027 -.067
20 895 633 154 179 741 454 894 637 157 179 740 458 0 0 171 125 33 42 100 100 98 98 1195 1198 1.632 .613 .619 .613 .619 1.462 80 341 .603 .848 100 4550 6070 94 104 362 372 0 671 190 481 .65 676 486 1.539 .656 -.622 -.607

Total number of rows: 41664

Table truncated, full table size 9500 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap