NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148722 Query DataSets for GSM148722
Status Public on Oct 03, 2007
Title PT233_4 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49682.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT233_4 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT233_4 DNA
Prostate genomic DNA; LabeledExtract: 49682.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 = 38.83; Parameter Scan Time = 10:10:52; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 150002; 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 = 38.83; Parameter Scan Time = 10:10:52; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514906; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.27; 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/2004-02/49682.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
1 725 717 139 171 586 546 750 761 142 168 611 590 0 0 135 180 28 42 100 96 100 96 1132 1201 1.073 .932 .966 .87 .989 1.681 32 226 .982 .853 70 1690 6280 116 123 81 88 0 685 163 521 .89 727 563 1.124 .922 -.169 -.117
2 964 679 137 165 827 514 998 704 140 164 861 539 0 0 229 180 31 43 100 100 100 96 1341 1400 1.609 .622 .626 .596 .638 1.45 32 226 .645 .838 70 1830 6280 116 123 95 102 0 648 158 491 .593 672 515 1.685 .598 -.753 -.743
3 1234 1389 137 169 1097 1220 1414 1544 140 167 1277 1375 0 0 402 438 33 40 100 100 100 100 2317 2652 .899 1.112 1.077 1.097 1.115 1.458 52 296 1.104 .911 80 1980 6280 116 124 110 118 0 1326 161 1165 1.062 1474 1313 .942 1.028 .086 .04
4 917 524 140 167 777 357 956 530 141 167 816 363 0 0 175 123 32 44 100 100 100 100 1134 1179 2.176 .459 .445 .442 .43 1.34 32 223 .465 .791 70 2130 6290 117 124 125 132 0 500 159 341 .439 506 347 2.28 .425 -1.189 -1.235
5 1444 1254 139 159 1305 1095 1539 1339 141 160 1400 1180 0 0 448 447 32 44 100 100 100 98 2400 2580 1.192 .839 .843 .789 .829 1.596 52 291 .863 .875 80 2280 6270 115 123 140 148 0 1197 152 1045 .801 1278 1127 1.248 .805 -.32 -.314
6 725 490 138 165 587 325 732 492 140 170 594 327 0 0 86 107 30 44 100 100 100 96 912 921 1.806 .554 .551 .516 .582 1.553 32 172 .544 .754 60 2420 6290 118 124 155 161 0 468 158 310 .529 470 312 1.892 .526 -.92 -.928
7 1188 1190 139 174 1049 1016 1204 1213 141 175 1065 1039 0 0 157 273 29 40 100 100 100 100 2065 2104 1.032 .969 .976 .926 .975 1.388 32 228 1.047 .89 70 2570 6280 116 123 169 176 0 1136 166 970 .925 1158 992 1.081 .931 -.113 -.103
8 1228 1350 142 167 1086 1183 1252 1378 144 168 1110 1211 0 0 151 209 35 43 100 100 100 100 2269 2321 .918 1.089 1.091 1.083 1.089 1.22 32 221 1.1 .869 70 2710 6280 116 123 183 190 0 1289 159 1129 1.04 1316 1156 .962 1.042 .057 .059
9 869 769 138 166 731 603 889 778 145 169 751 612 0 0 175 199 45 45 100 100 100 100 1334 1363 1.212 .825 .815 .8 .819 1.328 32 230 .853 .874 70 2860 6280 116 123 198 205 0 734 158 576 .788 743 584 1.27 .778 -.345 -.362
10 1103 1105 146 167 957 938 1212 1222 147 171 1066 1055 0 0 382 402 34 45 100 100 98 98 1895 2121 1.02 .98 .99 .945 .946 1.648 52 277 .982 .898 80 3010 6280 116 124 213 221 0 1055 159 896 .936 1167 1007 1.069 .945 -.096 -.082
11 775 802 142 163 633 639 804 805 143 167 662 642 0 0 146 136 34 45 100 100 100 100 1272 1304 .991 1.009 .97 1.014 1.001 1.254 32 220 1.009 .89 70 3150 6280 116 123 227 234 0 766 156 610 .964 769 613 1.038 .926 -.053 -.111
12 870 866 141 168 729 698 894 911 141 169 753 743 0 0 154 239 31 45 100 100 100 100 1427 1496 1.044 .957 .987 .907 .953 1.391 32 228 1.026 .848 70 3300 6280 116 123 242 249 0 827 160 666 .914 870 709 1.094 .942 -.13 -.086
13 1043 1308 141 164 902 1144 1103 1369 146 168 962 1205 0 0 223 310 41 51 100 100 100 100 2046 2167 .788 1.268 1.253 1.26 1.261 1.308 32 220 1.278 .913 70 3440 6280 116 123 256 263 0 1249 157 1092 1.211 1307 1150 .826 1.196 .276 .258
14 1100 1296 140 157 960 1139 1205 1432 146 162 1065 1275 0 0 352 445 38 48 100 100 98 100 2099 2340 .843 1.186 1.197 1.157 1.207 1.452 52 296 1.22 .915 80 3600 6280 116 124 272 280 0 1237 150 1087 1.133 1367 1217 .883 1.143 .18 .193
15 755 796 138 155 617 641 746 792 140 159 608 637 0 0 85 127 33 40 100 100 100 100 1258 1245 .963 1.039 1.048 1.026 1.06 1.305 32 214 1.046 .876 70 3740 6280 116 123 286 293 0 760 148 612 .992 756 608 1.008 1 -.012 0
16 1808 2232 136 150 1672 2082 1743 2257 137 155 1607 2107 0 0 948 1094 31 44 96 100 96 100 3754 3714 .803 1.245 1.311 1.314 1.227 1.614 52 282 1.224 .954 80 3890 6290 117 125 301 309 0 2131 143 1988 1.189 2155 2012 .841 1.252 .25 .324
17 1042 1213 139 154 903 1059 1019 1221 142 156 880 1067 0 0 236 281 33 39 100 100 100 100 1962 1947 .853 1.173 1.213 1.167 1.14 1.187 32 212 1.171 .927 70 4030 6280 116 123 315 322 0 1158 147 1011 1.12 1166 1019 .893 1.158 .163 .211
18 1253 1450 140 156 1113 1294 1318 1514 148 162 1178 1358 0 0 243 269 68 45 100 100 100 100 2407 2536 .86 1.163 1.153 1.167 1.15 1.187 32 224 1.153 .922 70 4180 6280 116 123 330 337 0 1384 149 1235 1.11 1445 1296 .901 1.101 .151 .138
19 2367 2627 138 150 2229 2477 2334 2613 141 151 2196 2463 0 0 812 1008 31 41 100 100 100 98 4706 4659 .9 1.111 1.122 1.063 1.095 1.426 52 278 1.126 .945 80 4320 6280 116 124 344 352 0 2508 143 2365 1.061 2495 2351 .943 1.071 .085 .099
20 950 810 140 152 810 658 929 847 144 155 789 695 0 0 311 263 34 41 100 98 98 98 1468 1484 1.231 .812 .881 .797 .809 1.321 52 290 .807 .912 80 4480 6280 116 124 360 368 0 773 145 628 .776 809 664 1.289 .841 -.367 -.25

Total number of rows: 41664

Table truncated, full table size 9485 Kbytes.




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