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Sample GSM148706 Query DataSets for GSM148706
Status Public on Oct 03, 2007
Title PT92_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49675.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT92_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT92_1 DNA
Prostate genomic DNA; LabeledExtract: 49675.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 = 38.86; Parameter Scan Time = 09:55:24; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148647; 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 = 38.86; Parameter Scan Time = 09:55:24; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513550; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.18; 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/2004-02/49675.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
1 949 788 162 181 787 607 952 808 162 180 790 627 0 0 153 177 38 46 100 100 100 100 1394 1417 1.297 .771 .794 .75 .774 1.358 32 226 .774 .851 70 1560 6080 84 91 52 59 0 659 151 508 .645 676 525 1.55 .664 -.632 -.591
2 1426 747 158 174 1268 573 1474 772 165 183 1316 598 0 0 390 244 37 48 100 100 100 100 1841 1914 2.213 .452 .454 .431 .446 1.464 32 171 .462 .825 60 1710 6080 85 91 68 74 0 625 146 479 .378 646 500 2.645 .38 -1.403 -1.395
3 1355 1670 159 170 1196 1500 1500 1818 161 169 1341 1648 0 0 512 647 36 47 100 100 98 100 2696 2989 .797 1.254 1.229 1.294 1.272 1.479 52 290 1.262 .953 80 1850 6090 85 93 81 89 0 1397 142 1255 1.049 1521 1379 .953 1.028 .07 .04
4 1366 602 155 169 1211 433 1483 604 159 172 1328 435 0 0 497 175 38 45 100 100 96 100 1644 1763 2.797 .358 .328 .396 .371 1.816 32 214 .331 .832 70 2000 6090 85 92 96 103 0 504 141 362 .299 505 364 3.342 .274 -1.741 -1.867
5 1588 1668 155 174 1433 1494 1594 1720 158 174 1439 1546 0 0 455 490 36 47 100 100 100 100 2927 2985 .959 1.043 1.074 1.038 1.042 1.231 52 284 1.042 .947 80 2140 6090 85 93 110 118 0 1396 146 1250 .872 1439 1294 1.146 .899 -.197 -.154
6 1225 272 157 171 1068 101 1349 254 160 171 1192 83 0 0 294 70 35 44 100 75 100 50 1169 1275 10.574 .095 .07 .08 .086 1.946 32 160 .077 .346 60 2300 6090 86 92 127 133 0 228 143 85 .079 213 69 12.637 .058 -3.66 -4.101
7 1150 1461 160 172 990 1289 1185 1541 163 177 1025 1369 0 0 363 496 35 48 100 100 100 100 2279 2394 .768 1.302 1.336 1.281 1.34 1.324 52 272 1.32 .934 80 2440 6090 85 93 140 148 0 1222 144 1079 1.089 1289 1146 .918 1.118 .124 .16
8 1471 1596 162 179 1309 1417 1458 1646 168 189 1296 1467 0 0 241 332 50 60 100 100 100 100 2726 2763 .924 1.083 1.132 1.069 1.082 1.238 32 218 1.097 .923 70 2580 6080 84 91 154 161 0 1335 150 1186 .906 1377 1228 1.104 .947 -.143 -.078
9 923 1027 168 170 755 857 909 983 172 175 741 813 0 0 267 318 47 52 100 100 98 100 1612 1554 .881 1.135 1.097 1.139 1.099 1.283 52 282 1.135 .915 80 2740 6090 85 93 170 178 0 859 142 717 .95 823 680 1.053 .918 -.074 -.123
10 1516 1419 164 178 1352 1241 1513 1376 168 181 1349 1198 0 0 338 441 43 51 100 100 100 100 2593 2547 1.089 .918 .888 .884 .909 1.252 52 314 1.138 .841 90 2880 6080 83 92 183 192 0 1187 149 1038 .768 1151 1002 1.302 .743 -.381 -.428
11 893 971 165 178 728 793 903 956 168 182 738 778 0 0 161 206 40 48 100 100 100 100 1521 1516 .918 1.089 1.054 1.077 1.037 1.283 32 221 1.011 .852 70 3030 6080 84 91 199 206 0 812 149 664 .911 800 651 1.097 .882 -.134 -.181
12 963 1149 164 180 799 969 941 1187 168 182 777 1007 0 0 553 585 43 58 100 100 100 100 1768 1784 .825 1.213 1.296 1.245 1.311 1.273 52 287 1.159 .936 80 3180 6090 85 93 214 222 0 961 151 811 1.015 993 843 .985 1.084 .021 .117
13 1068 1285 158 178 910 1107 1108 1330 160 185 950 1152 0 0 299 423 36 68 100 98 100 98 2017 2102 .822 1.216 1.213 1.151 1.226 1.511 52 296 1.208 .839 90 3330 6080 83 92 228 237 0 1075 149 926 1.018 1113 964 .982 1.015 .026 .021
14 1261 1563 155 174 1106 1389 1276 1596 158 174 1121 1422 0 0 472 568 36 44 100 100 100 100 2495 2543 .796 1.256 1.269 1.302 1.289 1.337 52 323 1.282 .885 90 3460 6080 83 92 241 250 0 1308 146 1162 1.051 1335 1190 .952 1.061 .072 .086
15 681 676 158 176 523 500 671 695 164 178 513 519 0 0 201 190 40 49 100 100 100 96 1023 1032 1.046 .956 1.012 .939 .964 1.284 52 285 .966 .914 80 3620 6080 84 92 258 266 0 566 147 418 .8 582 434 1.25 .847 -.322 -.24
16 1384 2020 165 176 1219 1844 1222 1743 167 179 1057 1567 0 0 777 1181 37 49 100 100 100 100 3063 2624 .661 1.513 1.482 1.503 1.422 1.385 52 279 1.532 .926 80 3770 6080 84 92 273 281 0 1690 147 1543 1.266 1458 1311 .79 1.24 .34 .311
17 815 863 163 168 652 695 860 840 164 176 697 672 0 0 217 222 37 54 100 100 100 100 1347 1369 .938 1.066 .964 1.076 1.157 1.39 32 208 1.052 .845 70 3910 6080 84 91 287 294 0 722 141 582 .892 703 562 1.121 .807 -.165 -.31
18 947 1029 160 175 787 854 922 1004 163 183 762 829 0 0 324 383 37 49 100 100 100 100 1641 1591 .922 1.085 1.088 1.07 1.063 1.372 52 269 1.103 .914 80 4060 6080 84 92 302 310 0 861 146 715 .908 840 694 1.101 .91 -.139 -.136
19 1885 2080 160 186 1725 1894 1688 1859 163 187 1528 1673 0 0 669 911 34 47 100 100 100 100 3619 3201 .911 1.098 1.095 1.059 1.113 1.304 52 300 1.144 .956 90 4200 6080 83 92 315 324 0 1740 156 1585 .919 1556 1400 1.088 .916 -.122 -.126
20 889 665 167 186 722 479 879 655 171 187 712 469 0 0 236 203 40 49 100 100 100 100 1201 1181 1.507 .663 .659 .639 .617 1.334 52 275 .683 .897 80 4340 6080 84 92 330 338 0 556 156 401 .555 548 392 1.801 .551 -.849 -.859

Total number of rows: 41664

Table truncated, full table size 9536 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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