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Sample GSM148704 Query DataSets for GSM148704
Status Public on Oct 03, 2007
Title PT205_3 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49673.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT205_3 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT205_3 DNA
Prostate genomic DNA; LabeledExtract: 49673.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 = 38.61; Parameter Scan Time = 09:26:53; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148618; 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 = 38.61; Parameter Scan Time = 09:26:53; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513521; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; 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/2004-02/49673.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
1 863 660 174 198 689 462 863 684 178 199 689 486 0 0 225 214 38 48 100 96 100 92 1151 1175 1.491 .671 .705 .602 .641 1.698 52 298 .706 .843 80 1660 5770 53 61 62 70 0 572 172 401 .582 593 422 1.719 .612 -.782 -.709
2 1487 752 172 202 1315 550 1558 802 173 205 1386 600 0 0 265 215 41 48 100 100 100 100 1865 1986 2.391 .418 .433 .387 .406 1.42 32 216 .413 .846 70 1810 5770 53 60 77 84 0 652 175 477 .363 696 520 2.757 .375 -1.463 -1.413
3 1365 1406 171 204 1194 1202 1403 1582 188 224 1232 1378 0 0 289 407 115 103 100 100 100 100 2396 2610 .993 1.007 1.119 .958 .996 1.308 32 226 1.03 .931 70 1940 5760 52 59 90 97 0 1219 177 1043 .873 1372 1195 1.145 .97 -.196 -.044
4 1377 591 162 205 1215 386 1436 589 166 205 1274 384 0 0 318 150 38 47 100 100 100 96 1601 1658 3.148 .318 .301 .302 .304 1.482 32 156 .324 .85 60 2110 5770 54 60 108 114 0 513 178 335 .276 511 333 3.629 .261 -1.86 -1.936
5 1449 1219 164 198 1285 1021 1503 1281 166 201 1339 1083 0 0 392 374 39 50 100 100 100 100 2306 2422 1.259 .795 .809 .775 .774 1.281 52 275 .794 .918 80 2230 5780 54 62 119 127 0 1057 172 886 .689 1111 939 1.451 .701 -.537 -.511
6 1204 571 167 192 1037 379 1242 582 170 198 1075 390 0 0 259 151 39 49 100 96 100 93 1416 1465 2.736 .365 .363 .336 .368 1.484 32 214 .373 .862 70 2410 5770 53 60 137 144 0 495 167 329 .317 505 338 3.155 .315 -1.658 -1.668
7 1051 1192 173 200 878 992 1122 1296 175 205 949 1096 0 0 260 365 43 49 100 100 100 100 1870 2045 .885 1.13 1.155 1.076 1.128 1.439 52 264 1.162 .925 80 2550 5770 53 61 151 159 0 1034 173 860 .98 1124 951 1.02 1.002 -.029 .002
8 1187 1150 172 205 1015 945 1267 1183 188 214 1095 978 0 0 250 341 91 69 100 100 100 100 1960 2073 1.074 .931 .893 .885 .969 1.44 32 201 .95 .879 70 2670 5760 52 59 163 170 0 997 178 820 .808 1026 848 1.238 .775 -.308 -.368
9 894 907 169 209 725 698 918 886 170 209 749 677 0 0 226 219 39 49 100 100 100 100 1423 1426 1.039 .963 .904 .969 .947 1.357 52 296 .958 .88 80 2840 5770 53 61 180 188 0 787 181 605 .835 768 587 1.198 .784 -.26 -.351
10 1436 1171 170 216 1266 955 1454 1204 186 222 1284 988 0 0 253 230 114 62 100 100 100 100 2221 2272 1.326 .754 .769 .747 .752 1.201 52 279 .742 .934 80 2990 5770 53 61 195 203 0 1016 187 828 .654 1044 857 1.528 .667 -.612 -.583
11 830 897 169 209 661 688 828 914 172 215 659 705 0 0 168 170 43 53 100 100 100 100 1349 1364 .961 1.041 1.07 1.041 1.03 1.312 32 206 1.032 .846 70 3120 5780 54 61 208 215 0 778 181 597 .903 793 611 1.108 .928 -.148 -.108
12 1023 990 166 219 857 771 1042 1020 186 237 876 801 0 0 154 202 150 146 100 100 100 93 1628 1677 1.112 .9 .914 .874 .909 1.303 32 231 .937 .902 70 3280 5760 52 59 224 231 0 859 190 669 .78 885 695 1.282 .793 -.358 -.334
13 1006 1292 164 221 842 1071 1021 1286 183 236 857 1065 0 0 154 302 150 137 100 100 98 100 1913 1922 .786 1.272 1.243 1.24 1.248 1.264 52 258 1.282 .894 80 3430 5770 53 61 239 247 0 1121 192 929 1.103 1115 924 .906 1.078 .142 .108
14 1230 1455 166 206 1064 1249 1247 1489 168 212 1081 1283 0 0 184 246 42 50 100 100 100 100 2313 2364 .852 1.174 1.187 1.167 1.184 1.229 52 249 1.184 .928 80 3560 5770 53 61 252 260 0 1262 179 1083 1.018 1291 1113 .982 1.029 .026 .042
15 738 781 165 214 573 567 770 794 166 216 605 580 0 0 138 161 34 51 100 100 100 100 1140 1185 1.011 .99 .959 .978 .962 1.351 52 264 1.002 .85 80 3710 5770 53 61 267 275 0 677 186 492 .858 689 503 1.165 .831 -.221 -.266
16 2071 2688 164 215 1907 2473 2131 2788 168 222 1967 2573 0 0 654 1009 59 56 100 100 100 100 4380 4540 .771 1.297 1.308 1.242 1.286 1.262 52 288 1.324 .962 80 3860 5770 53 61 282 290 0 2331 186 2145 1.125 2418 2232 .889 1.135 .17 .182
17 1146 1316 164 218 982 1098 1156 1348 179 230 992 1130 0 0 289 380 90 78 100 100 96 100 2080 2122 .894 1.118 1.139 1.103 1.148 1.402 32 226 1.127 .926 70 4010 5760 52 59 297 304 0 1141 189 952 .97 1169 980 1.031 .988 -.044 -.017
18 1165 1190 163 217 1002 973 1184 1263 166 220 1021 1046 0 0 232 300 41 53 100 100 100 100 1975 2067 1.03 .971 1.024 .929 .969 1.311 52 266 1.003 .921 80 4160 5770 53 61 312 320 0 1032 188 844 .842 1095 907 1.187 .889 -.248 -.17
19 2689 2113 163 211 2526 1902 2453 1846 166 217 2290 1635 0 0 1006 805 39 55 100 100 100 100 4428 3925 1.328 .753 .714 .747 .755 1.191 52 316 .755 .956 90 4300 5770 52 61 325 334 0 1833 183 1650 .653 1601 1418 1.531 .619 -.615 -.691
20 1105 892 161 209 944 683 1105 914 166 213 944 705 0 0 159 207 53 54 100 100 100 100 1627 1649 1.382 .724 .747 .689 .722 1.411 52 274 .753 .863 80 4450 5770 53 61 341 349 0 774 181 592 .628 793 611 1.594 .648 -.672 -.627

Total number of rows: 41664

Table truncated, full table size 9617 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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