NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148730 Query DataSets for GSM148730
Status Public on Oct 03, 2007
Title PT235_5 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52835.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT235_5 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT235_5 DNA
Prostate genomic DNA; LabeledExtract: 52835.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 = 1280, 5720; 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 = 39.11; Parameter Scan Time = 10:27:27; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 167909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; 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 = 39.11; Parameter Scan Time = 10:27:27; Parameter PMT Volts = 670; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 532813; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; 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/2004-06/52835.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 GPL4639
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
1 740 695 168 199 572 496 749 699 171 201 581 500 0 0 126 113 39 51 100 100 100 100 1068 1081 1.153 .867 .861 .868 .872 1.335 52 278 .866 .843 80 1790 6360 60 68 47 55 0 715 205 510 .892 719 514 1.121 .885 -.165 -.176
2 1075 1099 176 206 899 893 1071 1140 175 205 895 934 0 0 193 208 37 52 100 100 100 100 1792 1829 1.007 .993 1.044 .989 .987 1.204 52 274 1.002 .921 80 1940 6360 60 68 62 70 0 1130 212 919 1.022 1173 961 .979 1.073 .031 .102
3 614 695 167 193 447 502 601 707 171 197 434 514 0 0 114 115 38 52 100 100 100 100 949 948 .89 1.123 1.184 1.135 1.097 1.378 52 264 1.095 .824 80 2090 6360 60 68 77 85 0 715 199 516 1.155 727 529 .866 1.218 .208 .285
4 661 682 167 200 494 482 662 674 171 203 495 474 0 0 146 143 38 48 100 100 100 100 976 969 1.025 .976 .958 .976 1.005 1.319 52 254 .988 .833 80 2230 6360 60 68 91 99 0 702 206 496 1.004 693 488 .996 .985 .005 -.022
5 532 586 169 195 363 391 525 574 172 198 356 379 0 0 81 94 40 48 100 100 100 100 754 735 .928 1.077 1.065 1.073 1.141 1.374 52 325 1.08 .719 90 2380 6360 59 68 105 114 0 603 201 402 1.108 590 390 .903 1.095 .148 .131
6 632 661 166 180 466 481 641 661 169 188 475 481 0 0 102 123 38 53 100 100 100 100 947 956 .969 1.032 1.013 1.025 1.087 1.337 32 206 1.008 .829 70 2530 6360 60 67 121 128 0 680 185 495 1.062 680 495 .942 1.042 .086 .059
7 496 494 165 194 331 300 506 501 170 201 341 307 0 0 111 104 38 52 98 100 98 96 631 648 1.103 .906 .9 .887 .956 1.478 52 266 .886 .713 80 2670 6360 60 68 135 143 0 508 200 309 .932 515 316 1.073 .926 -.101 -.111
8 680 631 164 192 516 439 680 650 169 198 516 458 0 0 154 147 36 49 100 100 100 100 955 974 1.175 .851 .888 .842 .861 1.461 52 230 .855 .813 80 2820 6360 60 68 150 158 0 649 198 452 .875 669 471 1.143 .913 -.192 -.131
9 603 712 177 210 426 502 587 708 178 211 410 498 0 0 125 132 39 53 100 100 100 100 928 908 .849 1.178 1.215 1.188 1.171 1.424 80 289 1.179 .757 100 2960 6360 59 69 163 173 0 732 216 516 1.212 728 512 .825 1.249 .278 .321
10 1258 1475 181 225 1077 1250 1289 1447 183 227 1108 1222 0 0 251 264 43 55 100 100 100 100 2327 2330 .862 1.161 1.103 1.178 1.177 1.299 80 277 1.16 .909 100 3100 6360 59 69 177 187 0 1517 231 1286 1.194 1488 1257 .838 1.134 .256 .182
11 459 471 177 217 282 254 463 470 182 219 286 253 0 0 90 97 44 56 98 98 97 93 536 539 1.11 .901 .885 .892 .907 1.622 80 305 .974 .631 100 3250 6360 59 69 192 202 0 484 223 261 .927 483 260 1.079 .91 -.11 -.136
12 675 805 182 224 493 581 680 803 186 230 498 579 0 0 135 140 43 61 100 100 97 100 1074 1077 .849 1.178 1.163 1.206 1.189 1.378 80 323 1.177 .854 100 3400 6360 59 69 207 217 0 828 230 598 1.212 826 596 .825 1.196 .278 .258
13 758 968 186 240 572 728 767 984 190 243 581 744 0 0 168 184 41 69 98 100 97 98 1300 1325 .786 1.273 1.281 1.293 1.269 1.41 80 361 1.279 .848 110 3540 6360 58 69 220 231 0 996 247 749 1.309 1012 765 .764 1.317 .389 .398
14 941 964 187 232 754 732 902 943 192 235 715 711 0 0 186 173 49 70 100 100 100 100 1486 1426 1.03 .971 .994 .973 .962 1.22 80 360 .972 .89 110 3690 6360 58 69 235 246 0 992 239 753 .999 970 731 1.001 1.023 -.002 .033
15 461 476 186 235 275 241 452 464 195 239 266 229 0 0 96 99 52 73 100 97 100 85 516 495 1.141 .876 .861 .841 .867 1.708 80 302 .945 .597 100 3840 6360 59 69 251 261 0 490 242 248 .901 477 236 1.109 .886 -.15 -.175
16 3182 4146 185 228 2997 3918 3171 4189 194 238 2986 3961 0 0 745 764 54 76 100 100 100 100 6915 6947 .765 1.307 1.327 1.343 1.306 1.292 80 349 1.289 .943 110 3980 6360 58 69 264 275 0 4265 235 4030 1.345 4309 4074 .744 1.365 .427 .448
17 878 1028 181 234 697 794 879 1011 196 250 698 777 0 0 194 197 95 121 98 100 98 100 1491 1475 .878 1.139 1.113 1.164 1.162 1.344 80 358 1.76 .548 110 4130 6360 58 69 279 290 0 1057 241 817 1.172 1040 799 .853 1.145 .229 .195
18 1395 1700 181 247 1214 1453 1456 1676 211 287 1275 1429 0 0 323 304 130 171 100 100 100 100 2667 2704 .836 1.197 1.121 1.235 1.228 1.344 80 295 1.187 .918 100 4280 6360 59 69 295 305 0 1749 254 1495 1.231 1724 1470 .812 1.153 .3 .205
19 2668 2984 173 231 2495 2753 2722 3061 215 301 2549 2830 0 0 514 658 187 301 100 100 100 100 5248 5379 .906 1.103 1.11 1.093 1.103 1.3 80 316 1.124 .936 100 4420 6350 58 68 309 319 0 3069 238 2832 1.135 3149 2911 .881 1.142 .183 .192
20 984 983 177 226 807 757 996 1000 244 338 819 774 0 0 191 185 262 413 100 97 91 38 1564 1593 1.066 .938 .945 .94 .928 1.318 80 366 .942 .866 110 4570 6360 58 69 323 334 0 1011 232 779 .965 1029 796 1.036 .972 -.052 -.041

Total number of rows: 41472

Table truncated, full table size 9461 Kbytes.




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