NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148731 Query DataSets for GSM148731
Status Public on Oct 03, 2007
Title PT28_6 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52836.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT28_6 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT28_6 DNA
Prostate genomic DNA; LabeledExtract: 52836.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 = 39.21; Parameter Scan Time = 10:41:37; Parameter PMT Volts = 650; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 167923; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; 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 = 39.21; Parameter Scan Time = 10:41:37; Parameter PMT Volts = 690; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 532826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; 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/2004-06/52836.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
1 811 890 166 172 645 718 871 929 169 179 705 757 0 0 213 237 40 60 100 98 100 98 1363 1462 .898 1.113 1.074 1.098 1.151 1.521 52 286 1.128 .886 80 1740 6560 80 88 42 50 0 798 154 644 .999 833 679 1.001 .963 -.002 -.054
2 1068 1176 173 186 895 990 1149 1222 172 190 976 1036 0 0 369 400 38 59 98 100 98 100 1885 2012 .904 1.106 1.061 1.172 1.115 1.509 52 324 1.085 .905 90 1880 6560 79 88 55 64 0 1055 167 888 .992 1096 929 1.008 .952 -.011 -.07
3 727 770 171 178 556 592 719 774 174 182 548 596 0 0 112 151 40 52 100 100 100 100 1148 1144 .939 1.065 1.088 1.048 1.001 1.326 32 219 1.058 .816 70 2030 6560 80 87 71 78 0 691 160 531 .955 694 535 1.047 .976 -.066 -.035
4 820 801 171 204 649 597 850 782 180 206 679 578 0 0 237 201 43 58 100 100 100 100 1246 1257 1.087 .92 .851 .947 .934 1.369 52 265 .927 .861 80 2180 6570 81 89 86 94 0 719 183 536 .825 702 519 1.212 .764 -.277 -.389
5 698 674 180 205 518 469 690 679 187 218 510 474 0 0 109 125 49 85 100 100 100 96 987 984 1.104 .905 .929 .886 .866 1.376 52 274 .956 .747 80 2320 6560 80 88 100 108 0 605 184 421 .812 609 425 1.231 .834 -.3 -.262
6 749 877 188 221 561 656 753 840 216 273 565 619 0 0 138 208 201 322 100 100 87 40 1217 1184 .855 1.169 1.096 1.149 1.141 1.349 32 220 1.309 .746 70 2470 6560 80 87 115 122 0 787 198 589 1.049 754 555 .953 .983 .069 -.025
7 592 619 198 259 394 360 607 589 233 321 409 330 0 0 98 112 203 319 93 59 53 3 754 739 1.094 .914 .807 .911 .888 1.574 32 221 1.277 .694 70 2610 6560 80 87 129 136 0 555 232 323 .82 528 296 1.22 .724 -.287 -.466
8 737 758 190 234 547 524 753 775 203 248 563 541 0 0 197 183 76 92 100 98 96 94 1071 1104 1.044 .958 .961 .979 .959 1.688 52 264 .95 .799 80 2760 6560 80 88 144 152 0 680 210 470 .859 695 485 1.164 .862 -.219 -.214
9 725 922 174 193 551 729 757 979 181 204 583 786 0 0 159 252 47 69 100 98 100 97 1280 1369 .756 1.323 1.348 1.238 1.28 1.724 80 335 1.376 .857 100 2910 6560 79 89 158 168 0 827 173 654 1.187 878 705 .842 1.21 .247 .274
10 1599 1999 171 197 1428 1802 1668 2107 175 204 1497 1910 0 0 376 485 43 64 100 100 100 100 3230 3407 .792 1.262 1.276 1.257 1.277 1.263 80 319 1.266 .949 100 3050 6560 79 89 172 182 0 1793 177 1617 1.132 1890 1714 .883 1.145 .179 .195
11 641 721 176 196 465 525 665 726 180 199 489 530 0 0 147 181 42 59 100 100 98 100 990 1019 .886 1.129 1.084 1.119 1.093 1.468 80 328 1.161 .822 100 3200 6560 79 89 187 197 0 647 176 471 1.013 651 476 .987 .972 .019 -.04
12 814 1070 178 201 636 869 851 1141 183 205 673 940 0 0 230 310 44 64 100 98 100 97 1505 1613 .732 1.366 1.397 1.355 1.36 1.519 80 343 1.389 .873 100 3340 6560 79 89 201 211 0 960 180 780 1.226 1024 843 .816 1.253 .294 .326
13 1480 2251 186 223 1294 2028 1511 2260 195 232 1325 2037 0 0 191 283 115 91 100 100 100 100 3322 3362 .638 1.567 1.537 1.569 1.536 1.17 52 288 1.616 .852 90 3480 6560 79 88 215 224 0 2020 200 1819 1.406 2028 1828 .711 1.379 .492 .464
14 1487 2191 187 214 1300 1977 1523 2240 193 221 1336 2026 0 0 257 378 52 76 100 100 100 100 3277 3362 .658 1.521 1.516 1.527 1.529 1.237 80 351 1.529 .934 100 3630 6560 79 89 230 240 0 1966 192 1774 1.364 2010 1818 .733 1.361 .448 .444
15 678 1005 185 208 493 797 682 1025 192 217 497 817 0 0 126 171 53 78 100 100 100 100 1290 1314 .619 1.617 1.644 1.643 1.627 1.353 80 314 1.655 .854 100 3770 6560 79 89 244 254 0 902 187 715 1.45 920 733 .689 1.475 .536 .561
16 3897 6400 188 203 3709 6197 4165 6945 190 209 3977 6742 0 0 1092 1782 42 66 100 100 100 100 9906 10719 .599 1.671 1.695 1.698 1.666 1.28 80 338 1.67 .975 100 3920 6560 79 89 259 269 0 5742 182 5560 1.499 6231 6049 .667 1.521 .584 .605
17 949 1407 184 174 765 1233 976 1468 186 181 792 1294 0 0 229 405 42 58 100 100 98 100 1998 2086 .62 1.612 1.634 1.616 1.632 1.392 80 340 1.672 .917 100 4070 6560 79 89 274 284 0 1262 156 1106 1.446 1317 1161 .692 1.466 .532 .552
18 1680 2541 184 159 1496 2382 1683 2522 189 163 1499 2363 0 0 195 406 41 50 100 100 100 100 3878 3862 .628 1.592 1.576 1.582 1.613 1.208 52 312 1.632 .932 90 4220 6550 78 87 289 298 0 2280 143 2137 1.429 2263 2120 .7 1.414 .515 .5
19 2290 3061 215 183 2075 2878 2262 3089 550 812 2047 2906 0 0 279 360 1447 1659 98 100 0 9 4953 4953 .721 1.387 1.42 1.389 1.39 1.166 52 244 1.54 .844 80 4360 6560 80 88 304 312 0 2746 164 2582 1.244 2771 2607 .804 1.274 .315 .349
20 65167 65535 7677 8748 57490 56787 65535 65535 30577 29343 57858 56787 98 100 2655 0 30837 28980 100 100 0 0 114277 114645 1.012 .988 .981 .989 .981 1.057 52 246 .942 .917 80 4500 6550 79 87 318 326 -100 58796 7848 50948 .886 58796 50948 1.128 .881 -.174 -.184

Total number of rows: 41472

Table truncated, full table size 9626 Kbytes.




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