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Sample GSM148734 Query DataSets for GSM148734
Status Public on Oct 03, 2007
Title PT32_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47185.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT32_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT32_1 DNA
Prostate genomic DNA; LabeledExtract: 47185.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 = 680, 5080; 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 = 38.84; Parameter Scan Time = 09:28:20; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136773; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.49; 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 = 38.84; Parameter Scan Time = 09:28:20; Parameter PMT Volts = 660; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501838; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; 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/2003-12/47185.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
1 658 587 146 203 512 384 638 627 148 203 492 424 0 0 132 183 32 46 100 100 100 96 896 916 1.333 .75 .862 .667 .796 1.651 52 344 .815 .786 90 1670 5990 86 95 94 103 0 649 224 424 .829 693 468 1.207 .952 -.271 -.071
2 917 587 151 199 766 388 990 623 153 203 839 424 0 0 247 182 34 50 100 96 100 90 1154 1263 1.974 .507 .505 .443 .497 1.957 52 254 .513 .772 80 1810 5990 87 95 109 117 0 649 220 429 .56 688 468 1.787 .558 -.837 -.841
3 1065 924 149 207 916 717 1130 928 152 204 981 721 0 0 276 194 35 46 100 100 100 100 1633 1702 1.278 .783 .735 .808 .749 1.555 52 293 .746 .844 90 1940 6000 87 96 121 130 0 1021 229 792 .865 1025 797 1.156 .812 -.209 -.3
4 762 467 150 202 612 265 845 464 153 203 695 262 0 0 228 121 34 46 100 96 100 90 877 957 2.309 .433 .377 .419 .402 1.847 52 265 .411 .71 80 2090 5990 87 95 137 145 0 516 223 293 .478 513 289 2.09 .417 -1.064 -1.264
5 1217 935 149 198 1068 737 1219 927 155 204 1070 729 0 0 220 178 44 51 100 100 100 100 1805 1799 1.449 .69 .681 .685 .67 1.273 52 325 .691 .862 90 2230 5990 86 95 150 159 0 1033 219 814 .762 1024 805 1.312 .753 -.391 -.41
6 796 553 149 195 647 358 824 567 153 207 675 372 0 0 118 87 38 58 100 100 100 100 1005 1047 1.807 .553 .551 .545 .553 1.281 32 213 .521 .763 70 2380 5990 87 94 166 173 0 611 215 396 .611 626 411 1.636 .609 -.71 -.716
7 1009 989 146 200 863 789 997 999 149 201 851 799 0 0 151 184 34 49 100 100 100 100 1652 1650 1.094 .914 .939 .894 .95 1.327 52 326 .938 .883 90 2530 5990 86 95 180 189 0 1093 221 872 1.01 1104 883 .99 1.037 .015 .053
8 872 809 144 186 728 623 872 815 146 190 728 629 0 0 119 121 34 47 100 100 100 100 1351 1357 1.169 .856 .864 .85 .866 1.223 52 302 .838 .861 90 2680 5990 86 95 195 204 0 894 206 688 .946 900 695 1.058 .955 -.081 -.067
9 678 646 143 197 535 449 699 659 147 201 556 462 0 0 119 125 34 49 100 100 100 98 984 1018 1.192 .839 .831 .818 .777 1.515 52 310 .82 .773 90 2820 5990 86 95 209 218 0 714 218 496 .927 728 510 1.078 .918 -.109 -.123
10 1067 837 152 196 915 641 1062 848 155 204 910 652 0 0 190 157 37 54 100 100 100 100 1556 1562 1.427 .701 .716 .695 .723 1.28 52 301 .684 .863 90 2970 5990 86 95 224 233 0 925 217 708 .774 937 720 1.292 .792 -.37 -.337
11 622 575 156 194 466 381 630 577 158 201 474 383 0 0 102 97 38 53 100 100 100 100 847 857 1.223 .818 .808 .808 .836 1.33 52 296 .82 .778 90 3120 5990 86 95 239 248 0 635 214 421 .903 638 423 1.107 .893 -.147 -.164
12 788 753 156 201 632 552 780 760 156 208 624 559 0 0 134 125 32 52 100 100 100 100 1184 1183 1.145 .873 .896 .868 .882 1.325 52 257 .851 .834 80 3260 5990 87 95 254 262 0 832 222 610 .965 840 618 1.036 .99 -.051 -.015
13 874 958 154 191 720 767 921 997 158 199 767 806 0 0 198 185 39 52 100 100 100 100 1487 1573 .939 1.065 1.051 1.093 1.068 1.439 52 301 1.034 .885 90 3400 5990 86 95 267 276 0 1058 211 847 1.177 1102 891 .85 1.161 .235 .215
14 987 940 156 188 831 752 1043 997 158 193 887 809 0 0 248 259 38 53 100 100 100 100 1583 1696 1.105 .905 .912 .899 .888 1.556 80 401 .907 .87 100 3560 5990 86 96 283 293 0 1039 208 831 1 1102 894 1 1.008 0 .011
15 637 620 154 195 483 425 649 619 154 200 495 424 0 0 79 91 33 49 100 100 100 100 908 919 1.136 .88 .857 .869 .886 1.319 52 264 .883 .769 90 3710 5990 86 95 298 307 0 685 215 470 .972 684 468 1.029 .946 -.041 -.079
16 2165 2310 152 195 2013 2115 2407 2641 153 197 2255 2446 0 0 1001 991 34 52 98 100 98 100 4128 4701 .952 1.051 1.085 1.133 1.042 1.81 80 351 1.035 .943 100 3850 5990 86 96 312 322 0 2552 215 2337 1.161 2918 2703 .861 1.198 .215 .261
17 1125 1163 147 203 978 960 1149 1157 149 203 1002 954 0 0 179 194 30 52 100 100 100 100 1938 1956 1.019 .982 .952 .979 .957 1.259 52 254 .98 .885 80 4000 5990 87 95 328 336 0 1285 224 1061 1.085 1278 1054 .922 1.052 .117 .073
18 1161 967 148 203 1013 764 1150 966 151 205 1002 763 0 0 145 147 33 51 100 100 100 100 1777 1765 1.326 .754 .761 .746 .783 1.274 52 290 .739 .851 90 4150 5990 86 95 342 351 0 1068 224 844 .833 1067 843 1.2 .841 -.263 -.249
19 4699 4210 151 182 4548 4028 4118 3578 169 203 3967 3396 0 0 3002 2692 115 99 100 100 100 100 8576 7363 1.129 .886 .856 .869 .851 1.403 52 290 .879 .908 90 4280 5980 85 94 355 364 0 4652 201 4451 .979 3953 3752 1.022 .946 -.031 -.08
20 845 658 148 195 697 463 864 676 162 210 716 481 0 0 186 134 105 90 98 98 97 97 1160 1197 1.505 .664 .672 .648 .649 1.405 80 367 .654 .841 100 4440 5990 86 96 371 381 0 727 215 512 .734 747 531 1.362 .742 -.446 -.43

Total number of rows: 41664

Table truncated, full table size 9507 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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