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Sample GSM148736 Query DataSets for GSM148736
Status Public on Oct 03, 2007
Title PT315_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48740.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT315_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT315_2 DNA
Prostate genomic DNA; LabeledExtract: 48740.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 = 1080, 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 = 38.34; Parameter Scan Time = 10:24:13; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; 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 = 38.34; Parameter Scan Time = 10:24:13; Parameter PMT Volts = 660; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512743; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.05; 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/2004-01/48740.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
1 738 680 162 168 576 512 750 718 165 169 588 550 0 0 204 232 39 42 100 100 100 98 1088 1138 1.125 .889 .935 .826 .897 1.555 52 280 .936 .863 80 1900 6290 105 113 78 86 0 695 172 523 .908 734 562 1.101 .956 -.139 -.066
2 1078 906 169 178 909 728 1113 914 170 177 944 736 0 0 178 204 39 42 100 100 100 100 1637 1680 1.249 .801 .78 .78 .782 1.257 32 202 .819 .85 70 2020 6290 105 112 90 97 0 926 182 744 .818 934 752 1.222 .797 -.289 -.328
3 1201 1407 165 176 1036 1231 1207 1427 168 179 1042 1251 0 0 345 507 38 45 100 100 100 100 2267 2293 .842 1.188 1.201 1.113 1.215 1.362 52 296 1.242 .927 80 2180 6290 105 113 106 114 0 1437 180 1258 1.214 1458 1278 .824 1.227 .28 .295
4 997 781 168 166 829 615 1017 751 170 168 849 585 0 0 175 213 40 43 100 100 100 100 1444 1434 1.348 .742 .689 .711 .736 1.336 32 214 .76 .85 70 2320 6290 105 112 120 127 0 798 170 628 .758 767 598 1.319 .704 -.4 -.506
5 1232 1222 159 172 1073 1050 1232 1255 161 173 1073 1083 0 0 240 313 35 42 100 100 100 100 2123 2156 1.022 .979 1.009 .953 .999 1.248 52 334 1.044 .878 90 2470 6290 104 113 134 143 0 1248 176 1073 1 1282 1106 1 1.031 0 .044
6 768 709 158 173 610 536 804 756 159 174 646 583 0 0 160 127 33 41 100 100 100 100 1146 1229 1.138 .879 .902 .887 .872 1.256 32 212 .846 .848 70 2600 6290 105 112 148 155 0 724 177 548 .898 772 596 1.114 .922 -.156 -.117
7 1004 969 157 163 847 806 1012 983 160 168 855 820 0 0 198 233 36 44 100 100 100 100 1653 1675 1.051 .952 .959 .935 .924 1.311 52 272 .96 .887 80 2760 6290 105 113 164 172 0 990 167 823 .972 1004 838 1.029 .98 -.041 -.029
8 905 934 158 164 747 770 862 956 168 172 704 792 0 0 196 187 63 47 100 100 100 100 1517 1496 .97 1.031 1.125 1.031 1.03 1.255 52 255 1.022 .892 80 2900 6290 105 113 178 186 0 954 168 787 1.053 977 809 .95 1.149 .075 .201
9 675 849 159 165 516 684 634 886 164 167 475 721 0 0 171 231 63 47 100 100 100 100 1200 1196 .754 1.326 1.518 1.313 1.288 1.431 52 254 1.352 .859 80 3050 6290 105 113 193 201 0 867 169 699 1.354 905 737 .738 1.551 .437 .633
10 1033 1136 156 163 877 973 1055 1173 159 166 899 1010 0 0 307 283 39 45 100 100 100 100 1850 1909 .901 1.109 1.123 1.14 1.116 1.297 52 255 1.059 .895 80 3190 6290 105 113 207 215 0 1161 167 994 1.133 1198 1032 .882 1.148 .181 .199
11 583 613 164 176 419 437 560 591 172 184 396 415 0 0 124 154 81 93 100 100 100 100 856 811 .959 1.043 1.048 1.023 1.041 1.381 52 276 1.112 .792 80 3340 6290 105 113 222 230 0 626 180 446 1.065 604 424 .939 1.071 .092 .098
12 686 741 161 161 525 580 684 745 171 176 523 584 0 0 210 219 81 94 98 100 94 98 1105 1107 .905 1.105 1.117 1.137 1.134 1.591 52 274 1.095 .841 80 3490 6290 105 113 237 245 0 757 164 593 1.129 761 597 .886 1.141 .175 .19
13 737 966 155 165 582 801 783 1012 161 170 628 847 0 0 218 276 37 44 100 100 100 100 1383 1475 .727 1.376 1.349 1.41 1.391 1.39 52 251 1.367 .89 80 3630 6290 105 113 251 259 0 987 169 818 1.406 1034 865 .711 1.378 .492 .462
14 999 1264 158 174 841 1090 986 1271 161 176 828 1097 0 0 158 313 33 44 100 100 100 100 1931 1925 .772 1.296 1.325 1.26 1.345 1.294 52 275 1.351 .904 80 3790 6290 105 113 267 275 0 1291 178 1114 1.324 1298 1121 .755 1.354 .405 .437
15 528 548 156 168 372 380 526 546 160 167 370 378 0 0 118 123 37 42 100 100 98 100 752 748 .979 1.022 1.022 1.021 .979 1.453 52 242 1.042 .801 80 3930 6290 105 113 281 289 0 560 172 388 1.044 558 386 .958 1.044 .062 .062
16 1762 2377 157 170 1605 2207 1506 2066 159 173 1349 1896 0 0 767 1036 36 45 100 100 100 100 3812 3245 .727 1.375 1.405 1.372 1.365 1.31 52 288 1.379 .936 80 4080 6290 105 113 296 304 0 2428 174 2255 1.405 2111 1937 .712 1.436 .49 .522
17 800 912 160 173 640 739 753 885 161 174 593 712 0 0 218 227 36 42 100 100 100 100 1379 1305 .866 1.155 1.201 1.162 1.223 1.282 32 207 1.16 .905 70 4230 6280 104 111 311 318 0 932 177 755 1.18 904 727 .848 1.227 .238 .295
18 801 887 160 174 641 713 786 880 162 177 626 706 0 0 268 216 35 45 98 100 98 100 1354 1332 .899 1.112 1.128 1.21 1.123 1.553 52 277 1.048 .853 80 4370 6290 105 113 325 333 0 906 178 728 1.136 899 721 .88 1.152 .184 .204
19 1801 2119 159 172 1642 1947 1830 2213 161 176 1671 2041 0 0 491 719 40 47 100 100 100 100 3589 3712 .843 1.186 1.221 1.091 1.194 1.502 52 337 1.234 .938 90 4520 6280 103 112 339 348 0 2165 176 1989 1.211 2261 2085 .826 1.248 .277 .319
20 710 686 162 180 548 506 702 698 162 182 540 518 0 0 131 124 38 44 100 100 100 100 1054 1058 1.083 .923 .959 .921 .917 1.306 52 258 .899 .849 80 4670 6290 105 113 355 363 0 701 184 517 .943 713 529 1.06 .98 -.084 -.029

Total number of rows: 41664

Table truncated, full table size 9444 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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