NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148705 Query DataSets for GSM148705
Status Public on Oct 03, 2007
Title PT335_6 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49674.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT335_6 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT335_6 DNA
Prostate genomic DNA; LabeledExtract: 49674.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 = 1000, 5200; 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 = 38.71; Parameter Scan Time = 09:42:28; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148633; 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 = 38.71; Parameter Scan Time = 09:42:28; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513537; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.20; 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/2004-02/49674.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 1036 887 172 212 864 675 1050 904 178 215 878 692 0 0 153 171 43 49 100 100 100 100 1539 1570 1.28 .781 .788 .766 .784 1.268 32 230 .754 .867 70 1630 6320 108 115 59 66 0 831 199 632 .732 847 648 1.366 .738 -.45 -.437
2 1617 896 172 206 1445 690 1699 981 175 207 1527 775 0 0 323 267 39 54 100 100 100 100 2135 2302 2.094 .478 .508 .439 .47 1.444 32 224 .483 .877 70 1780 6330 109 116 74 81 0 840 193 647 .447 919 726 2.235 .476 -1.16 -1.072
3 1512 1638 171 201 1341 1437 1689 1770 172 204 1518 1569 0 0 473 492 39 48 100 100 100 100 2778 3087 .933 1.072 1.034 1.09 1.052 1.367 52 289 1.068 .955 80 1920 6330 109 117 88 96 0 1535 188 1346 1.004 1658 1470 .996 .968 .006 -.046
4 1540 642 170 203 1370 439 1598 670 174 209 1428 467 0 0 336 159 38 47 100 100 100 100 1809 1895 3.121 .32 .327 .306 .324 1.529 32 170 .306 .797 60 2070 6330 110 116 104 110 0 602 190 411 .3 628 438 3.331 .306 -1.736 -1.706
5 1936 1642 163 198 1773 1444 1993 1629 166 199 1830 1431 0 0 567 430 37 50 100 100 100 100 3217 3261 1.228 .814 .782 .838 .802 1.299 52 344 .8 .949 90 2210 6330 108 117 116 125 0 1539 186 1353 .763 1526 1341 1.31 .733 -.39 -.449
6 1407 654 164 209 1243 445 1490 680 167 214 1326 471 0 0 401 186 35 53 100 96 100 96 1688 1797 2.793 .358 .355 .346 .358 1.452 32 214 .348 .819 70 2360 6330 109 116 132 139 0 613 196 417 .335 637 441 2.981 .333 -1.576 -1.587
7 1165 1248 165 211 1000 1037 1228 1348 166 214 1063 1137 0 0 337 393 36 49 100 98 100 98 2037 2200 .964 1.037 1.07 .985 1.082 1.658 52 284 1.056 .927 80 2510 6330 109 117 147 155 0 1169 198 972 .972 1263 1065 1.029 1.002 -.042 .003
8 1286 1235 168 200 1118 1035 1389 1289 171 207 1221 1089 0 0 364 353 40 54 100 100 100 100 2153 2310 1.08 .926 .892 .919 .917 1.439 52 268 .918 .923 80 2660 6330 109 117 162 170 0 1157 187 970 .867 1208 1020 1.153 .836 -.205 -.259
9 1023 1039 169 214 854 825 1025 1033 172 219 856 819 0 0 244 254 48 59 100 100 100 100 1679 1675 1.035 .966 .957 .956 .933 1.395 32 213 .962 .855 70 2800 6320 108 115 176 183 0 974 201 773 .905 968 767 1.105 .896 -.144 -.158
10 1589 1306 164 217 1425 1089 1620 1333 169 218 1456 1116 0 0 336 283 45 50 100 100 100 100 2514 2572 1.309 .764 .766 .758 .766 1.243 52 266 .758 .946 80 2950 6330 109 117 191 199 0 1224 203 1020 .716 1249 1046 1.397 .718 -.482 -.478
11 870 885 162 210 708 675 935 939 164 208 773 729 0 0 283 221 35 52 98 100 98 100 1383 1502 1.049 .953 .943 .988 .935 1.351 52 262 .929 .91 80 3090 6330 109 117 205 213 0 829 197 632 .893 880 683 1.119 .884 -.163 -.178
12 1073 1067 163 208 910 859 1124 1112 168 210 961 904 0 0 287 260 49 52 100 100 100 100 1769 1865 1.059 .944 .941 .956 .926 1.441 52 274 .934 .913 80 3250 6330 109 117 221 229 0 1000 195 805 .884 1042 847 1.131 .881 -.177 -.182
13 1131 1367 157 216 974 1151 1183 1421 160 215 1026 1205 0 0 348 368 38 52 100 100 98 100 2125 2231 .846 1.182 1.174 1.238 1.171 1.369 52 248 1.165 .937 80 3390 6330 109 117 235 243 0 1281 202 1078 1.107 1331 1129 .903 1.1 .147 .138
14 1341 1208 159 202 1182 1006 1385 1193 163 207 1226 991 0 0 278 252 34 50 100 100 100 100 2188 2217 1.175 .851 .808 .843 .86 1.287 52 274 .845 .922 80 3540 6330 109 117 250 258 0 1132 189 943 .797 1118 929 1.254 .757 -.327 -.401
15 924 979 164 214 760 765 901 1031 168 218 737 817 0 0 188 169 39 51 100 100 100 100 1525 1554 .993 1.007 1.109 1.021 1.015 1.26 32 214 1.01 .911 70 3680 6320 108 115 264 271 0 917 201 717 .943 966 766 1.06 1.039 -.084 .055
16 2298 3116 158 212 2140 2904 2518 3405 162 214 2360 3193 0 0 887 1117 40 51 100 100 100 100 5044 5553 .737 1.357 1.353 1.393 1.368 1.273 52 296 1.341 .962 80 3830 6320 108 116 279 287 0 2920 199 2721 1.271 3190 2992 .786 1.268 .347 .342
17 1330 1471 158 207 1172 1264 1341 1497 165 214 1183 1290 0 0 252 280 43 64 100 100 100 100 2436 2473 .927 1.078 1.09 1.079 1.114 1.234 32 213 1.074 .923 70 3980 6320 108 115 294 301 0 1378 194 1184 1.011 1403 1209 .99 1.022 .015 .031
18 1260 1410 160 207 1100 1203 1368 1518 164 212 1208 1311 0 0 381 406 39 52 100 100 100 100 2303 2519 .914 1.094 1.085 1.099 1.072 1.278 52 254 1.083 .941 80 4130 6330 109 117 309 317 0 1321 194 1127 1.025 1422 1228 .976 1.017 .035 .024
19 3108 3283 160 213 2948 3070 3296 3343 164 216 3136 3130 0 0 850 792 40 51 100 100 100 100 6018 6266 .96 1.041 .998 1.078 1.014 1.347 52 257 1.025 .96 80 4270 6330 109 117 323 331 0 3076 200 2876 .976 3132 2933 1.025 .935 -.035 -.097
20 1261 1047 156 209 1105 838 1301 1073 163 214 1145 864 0 0 340 204 44 60 100 100 100 100 1943 2009 1.319 .758 .755 .792 .748 1.388 52 306 .736 .926 90 4410 6330 108 117 336 345 0 981 196 785 .711 1005 810 1.407 .707 -.493 -.5

Total number of rows: 41664

Table truncated, full table size 9537 Kbytes.




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