NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148757 Query DataSets for GSM148757
Status Public on Oct 03, 2007
Title PT173_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47161.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT173_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT173_2 DNA
Prostate genomic DNA; LabeledExtract: 47161.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 = 39.37; Parameter Scan Time = 12:59:49; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134350; 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 = 39.37; Parameter Scan Time = 12:59:49; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.26; 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/2003-11/47161.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
1 946 1014 151 243 795 771 928 1069 153 251 777 826 0 0 134 259 34 52 100 100 100 100 1566 1603 1.031 .97 1.063 .89 1.003 1.552 32 225 1.005 .844 70 1740 5760 64 71 82 89 0 912 219 694 .872 962 743 1.146 .956 -.197 -.065
2 1369 996 144 258 1225 738 1378 1046 149 258 1234 788 0 0 284 204 35 46 100 100 100 100 1963 2022 1.66 .602 .639 .597 .609 1.253 32 220 .611 .908 70 1900 5760 64 71 98 105 0 896 232 664 .542 941 709 1.845 .574 -.884 -.8
3 1469 1764 153 242 1316 1522 1610 1874 154 247 1457 1632 0 0 421 484 34 46 100 100 100 100 2838 3089 .865 1.157 1.12 1.159 1.218 1.415 52 285 1.154 .926 80 2040 5770 65 73 112 120 0 1587 218 1369 1.04 1686 1468 .961 1.008 .057 .011
4 1240 753 151 245 1089 508 1291 785 151 252 1140 540 0 0 234 196 34 46 100 100 100 96 1597 1680 2.144 .466 .474 .433 .494 1.451 32 203 .476 .847 70 2200 5760 64 71 128 135 0 677 220 457 .42 706 486 2.383 .426 -1.253 -1.231
5 1512 1444 148 242 1364 1202 1576 1527 151 247 1428 1285 0 0 290 350 34 50 100 100 100 100 2566 2713 1.135 .881 .9 .856 .865 1.253 52 340 .905 .918 90 2320 5760 63 72 139 148 0 1299 218 1081 .793 1374 1156 1.262 .809 -.335 -.305
6 950 721 145 241 805 480 929 694 149 244 784 453 0 0 170 185 35 51 100 100 100 96 1285 1237 1.677 .596 .578 .559 .611 1.426 32 220 .627 .841 70 2490 5760 64 71 157 164 0 649 217 432 .536 624 407 1.864 .52 -.899 -.944
7 1242 1454 147 247 1095 1207 1272 1491 150 251 1125 1244 0 0 297 254 32 54 100 100 100 100 2302 2369 .907 1.102 1.106 1.126 1.114 1.255 52 297 1.086 .91 90 2630 5770 64 73 170 179 0 1308 222 1086 .991 1341 1119 1.009 .995 -.012 -.008
8 1255 694 149 249 1106 445 1244 687 152 249 1095 438 0 0 234 169 32 52 100 100 100 96 1551 1533 2.485 .402 .4 .376 .386 1.468 52 303 .417 .834 90 2770 5760 63 72 184 193 0 624 224 400 .362 618 394 2.763 .36 -1.466 -1.475
9 854 969 149 242 705 727 861 996 154 249 712 754 0 0 148 210 37 58 100 100 100 98 1432 1466 .97 1.031 1.059 .979 1.06 1.516 52 254 1.085 .858 80 2920 5760 64 72 200 208 0 872 218 654 .928 896 678 1.078 .953 -.108 -.07
10 1349 1325 150 244 1199 1081 1346 1363 153 254 1196 1119 0 0 194 315 37 53 100 100 100 100 2280 2315 1.109 .902 .936 .863 .901 1.336 52 302 .93 .909 90 3060 5760 63 72 213 222 0 1192 219 972 .811 1226 1007 1.233 .842 -.302 -.249
11 798 895 152 244 646 651 801 910 153 247 649 666 0 0 168 224 32 48 100 100 100 100 1297 1315 .992 1.008 1.026 .97 1.043 1.44 52 276 1.042 .848 80 3210 5760 64 72 229 237 0 805 219 586 .906 819 599 1.103 .923 -.142 -.116
12 915 1058 152 240 763 818 929 1052 152 243 777 812 0 0 213 447 32 49 100 100 100 100 1581 1589 .933 1.072 1.045 1.002 .989 1.428 52 277 1.247 .765 80 3360 5760 64 72 244 252 0 952 216 736 .964 946 730 1.037 .94 -.052 -.089
13 1268 1186 153 243 1115 943 1271 1197 156 245 1118 954 0 0 234 230 34 47 100 100 100 100 2058 2072 1.182 .846 .853 .837 .822 1.261 52 230 .847 .895 80 3510 5760 64 72 259 267 0 1067 219 848 .761 1077 858 1.315 .768 -.395 -.382
14 1256 1529 153 237 1103 1292 1274 1630 156 240 1121 1393 0 0 269 319 36 52 100 100 100 100 2395 2514 .854 1.171 1.243 1.172 1.212 1.251 52 320 1.184 .916 90 3630 5760 63 72 270 279 0 1375 213 1162 1.054 1466 1253 .949 1.118 .075 .161
15 697 823 150 237 547 586 710 839 165 251 560 602 0 0 124 134 150 218 100 100 96 82 1133 1162 .933 1.071 1.075 1.068 1.083 1.256 52 280 1.094 .882 80 3800 5760 64 72 288 296 0 740 213 527 .964 755 541 1.038 .967 -.053 -.048
16 2441 3439 149 243 2292 3196 2379 3522 153 245 2230 3279 0 0 1014 1395 35 49 100 100 100 100 5488 5509 .717 1.394 1.47 1.382 1.375 1.199 52 326 1.4 .953 90 3940 5760 63 72 301 310 0 3093 219 2875 1.254 3168 2949 .797 1.323 .327 .403
17 1097 1362 152 231 945 1131 1099 1504 154 230 947 1273 0 0 316 391 36 48 100 100 100 100 2076 2220 .836 1.197 1.344 1.183 1.174 1.366 52 263 1.216 .911 80 4100 5760 64 72 318 326 0 1225 208 1017 1.077 1353 1145 .929 1.209 .106 .274
18 1153 1324 154 235 999 1089 1176 1380 158 234 1022 1145 0 0 197 244 37 46 100 100 100 100 2088 2167 .917 1.09 1.12 1.078 1.098 1.208 52 232 1.116 .93 80 4240 5760 64 72 332 340 0 1191 211 980 .981 1241 1030 1.02 1.008 -.028 .011
19 2239 2519 149 233 2090 2286 2381 2681 153 235 2232 2448 0 0 915 1001 35 47 100 100 97 98 4376 4680 .914 1.094 1.097 1.132 1.109 1.698 80 340 1.092 .954 100 4380 5760 63 73 345 355 0 2266 210 2056 .984 2412 2202 1.016 .987 -.023 -.02
20 1426 622 151 231 1275 391 1447 646 153 233 1296 415 0 0 301 151 34 45 100 94 100 94 1666 1711 3.261 .307 .32 .287 .31 1.586 52 300 .307 .818 90 4510 5760 63 72 358 367 0 559 208 352 .276 581 373 3.625 .288 -1.858 -1.796

Total number of rows: 41664

Table truncated, full table size 9638 Kbytes.




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