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Sample GSM148715 Query DataSets for GSM148715
Status Public on Oct 03, 2007
Title PT311_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47174.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT311_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT311_2 DNA
Prostate genomic DNA; LabeledExtract: 47174.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 = 880, 5320; 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 = 38.42; Parameter Scan Time = 10:17:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136023; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; 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 = 38.42; Parameter Scan Time = 10:17:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501088; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.16; 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/2003-12/47174.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 1101 506 158 175 943 331 1083 509 161 179 925 334 0 0 255 112 36 43 100 100 100 100 1274 1259 2.849 .351 .361 .344 .36 1.329 52 286 .333 .816 80 1690 6020 66 74 77 85 0 525 181 343 .364 528 346 2.748 .374 -1.458 -1.418
2 1074 765 153 173 921 592 1100 815 159 176 947 642 0 0 343 208 36 42 100 100 100 100 1513 1589 1.556 .643 .678 .65 .652 1.413 52 268 .621 .886 80 1830 6020 66 74 91 99 0 793 179 614 .666 845 666 1.501 .703 -.586 -.509
3 1190 1124 152 171 1038 953 1205 1155 157 174 1053 984 0 0 162 208 36 41 100 100 100 100 1991 2037 1.089 .918 .934 .903 .918 1.226 52 312 .942 .912 90 1980 6020 65 74 105 114 0 1165 177 988 .952 1197 1020 1.051 .969 -.071 -.046
4 812 522 153 178 659 344 833 508 158 179 680 330 0 0 203 139 37 45 100 96 100 94 1003 1010 1.916 .522 .485 .491 .526 1.675 52 265 .515 .775 80 2120 6020 66 74 120 128 0 541 185 357 .541 527 342 1.848 .503 -.886 -.991
5 1092 901 152 178 940 723 1119 940 159 183 967 762 0 0 283 276 58 53 100 96 100 96 1663 1729 1.3 .769 .788 .7 .77 1.86 80 380 .793 .893 100 2270 6020 65 75 134 144 0 934 185 750 .797 974 790 1.254 .817 -.327 -.292
6 772 592 156 173 616 419 821 607 156 179 665 434 0 0 174 160 34 46 100 100 98 96 1035 1099 1.47 .68 .653 .657 .673 1.598 52 233 .672 .811 80 2410 6020 66 74 149 157 0 614 179 434 .705 629 450 1.418 .677 -.504 -.564
7 953 852 158 175 795 677 957 853 159 180 799 678 0 0 178 151 36 46 100 100 100 100 1472 1477 1.174 .852 .849 .852 .821 1.319 52 301 .832 .876 90 2550 6020 65 74 162 171 0 883 181 702 .883 884 703 1.133 .88 -.18 -.185
8 750 709 154 180 596 529 753 759 156 184 599 579 0 0 196 209 37 46 100 93 100 93 1125 1178 1.127 .888 .967 .858 .929 1.712 80 347 .917 .85 100 2710 6020 65 75 178 188 0 735 187 548 .92 787 600 1.087 1.002 -.12 .003
9 713 589 158 179 555 410 719 605 158 183 561 426 0 0 224 155 37 42 98 98 97 97 965 987 1.354 .739 .759 .749 .788 1.688 80 320 .71 .813 100 2860 6020 65 75 193 203 0 611 186 425 .766 627 442 1.306 .787 -.385 -.345
10 1017 895 156 172 861 723 1034 933 166 181 878 761 0 0 220 173 104 58 98 100 97 100 1584 1639 1.191 .84 .867 .853 .859 1.327 80 349 .815 .909 100 3000 6020 65 75 207 217 0 928 178 750 .871 967 789 1.149 .899 -.2 -.154
11 589 555 153 170 436 385 592 564 156 175 439 394 0 0 96 92 36 42 100 100 100 100 821 833 1.132 .883 .897 .88 .844 1.306 52 300 .897 .833 90 3160 6020 65 74 223 232 0 575 176 399 .915 585 408 1.092 .93 -.127 -.104
12 651 593 157 178 494 415 701 601 159 179 544 423 0 0 210 179 38 42 100 98 95 97 909 967 1.19 .84 .778 .84 .834 1.672 80 346 .843 .839 100 3300 6020 65 75 237 247 0 615 185 430 .871 623 439 1.148 .806 -.199 -.311
13 735 788 157 174 578 614 774 837 160 177 617 663 0 0 172 212 37 43 100 98 98 98 1192 1280 .941 1.062 1.075 1.061 1.096 1.568 80 344 1.096 .87 100 3450 6020 65 75 252 262 0 817 180 637 1.101 868 687 .908 1.114 .139 .156
14 900 908 156 174 744 734 940 932 161 176 784 758 0 0 189 217 35 41 100 97 100 97 1478 1542 1.014 .987 .967 .932 .968 1.72 80 369 .998 .887 100 3600 6020 65 75 267 277 0 941 180 761 1.023 966 786 .978 1.002 .032 .003
15 580 574 160 175 420 399 601 575 161 175 441 400 0 0 89 88 35 42 100 100 100 100 819 841 1.053 .95 .907 .952 .975 1.389 52 278 .954 .796 90 3750 6020 65 74 282 291 0 595 181 414 .985 596 415 1.015 .94 -.022 -.089
16 1976 2157 157 169 1819 1988 2236 2392 162 174 2079 2223 0 0 914 973 66 51 97 100 96 98 3807 4302 .915 1.093 1.069 1.114 1.114 1.896 80 369 1.089 .94 100 3890 6020 65 75 296 306 0 2236 175 2061 1.133 2480 2305 .883 1.108 .18 .149
17 964 1122 152 166 812 956 965 1125 154 171 813 959 0 0 196 216 33 40 100 100 100 100 1768 1772 .849 1.177 1.18 1.182 1.168 1.221 52 240 1.158 .92 80 4030 6020 66 74 311 319 0 1163 172 991 1.221 1166 994 .819 1.223 .288 .29
18 939 974 157 173 782 801 932 985 161 179 775 812 0 0 132 177 37 45 100 100 100 100 1583 1587 .976 1.024 1.048 1.005 1.018 1.296 52 323 1.053 .891 90 4190 6010 64 73 326 335 0 1010 179 830 1.062 1021 842 .942 1.086 .087 .119
19 2520 2452 159 169 2361 2283 2515 2551 162 174 2356 2382 0 0 715 711 35 44 100 100 100 100 4644 4738 1.034 .967 1.011 .94 .962 1.547 80 346 .971 .91 100 4340 6020 65 75 341 351 0 2542 175 2367 1.002 2645 2469 .998 1.048 .004 .068
20 768 633 153 166 615 467 799 649 157 169 646 483 0 0 124 115 38 38 100 100 100 100 1082 1129 1.317 .759 .748 .748 .775 1.339 80 348 .764 .885 100 4480 6020 65 75 355 365 0 656 172 484 .787 673 501 1.27 .775 -.345 -.368

Total number of rows: 41664

Table truncated, full table size 9616 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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