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Sample GSM148733 Query DataSets for GSM148733
Status Public on Oct 03, 2007
Title PT148_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47183.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT148_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT148_1 DNA
Prostate genomic DNA; LabeledExtract: 47183.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 = 800, 4760; 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 = 39.11; Parameter Scan Time = 09:53:31; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136798; 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 = 39.11; Parameter Scan Time = 09:53:31; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501863; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; 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/2003-12/47183.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
1 758 578 163 170 595 408 744 586 165 175 581 416 0 0 114 127 34 47 100 100 100 98 1003 997 1.458 .686 .716 .655 .682 1.549 52 344 .685 .743 90 1560 6080 127 136 71 80 0 751 221 530 .891 761 540 1.123 .93 -.167 -.105
2 1113 632 163 174 950 458 1160 639 164 178 997 465 0 0 224 150 34 49 100 100 100 100 1408 1462 2.074 .482 .466 .467 .488 1.337 52 255 .473 .883 80 1700 6080 128 136 86 94 0 821 226 595 .626 830 604 1.597 .606 -.675 -.723
3 1581 1188 165 179 1416 1009 1595 1234 166 183 1430 1055 0 0 267 291 35 51 100 100 100 100 2425 2485 1.403 .713 .738 .686 .73 1.3 52 255 .718 .919 80 1840 6080 128 136 100 108 0 1543 232 1310 .925 1603 1370 1.081 .958 -.112 -.062
4 870 478 158 170 712 308 883 475 158 173 725 305 0 0 201 111 34 50 100 100 100 98 1020 1030 2.312 .433 .421 .42 .436 1.446 52 265 .43 .827 80 1990 6080 128 136 115 123 0 621 221 400 .562 617 396 1.78 .546 -.832 -.872
5 1428 1042 154 164 1274 878 1477 1032 154 168 1323 868 0 0 395 280 33 46 100 98 100 98 2152 2191 1.451 .689 .656 .685 .688 1.446 80 361 .678 .909 100 2140 6080 127 137 129 139 0 1353 213 1140 .895 1340 1127 1.117 .852 -.16 -.231
6 695 464 150 165 545 299 730 461 154 169 580 296 0 0 178 115 35 46 100 100 100 96 844 876 1.823 .549 .51 .538 .546 1.607 52 233 .509 .707 80 2280 6080 128 136 144 152 0 603 214 388 .713 599 384 1.403 .663 -.489 -.593
7 989 791 158 159 831 632 1085 834 160 163 927 675 0 0 376 284 35 48 97 98 96 95 1463 1602 1.315 .761 .728 .799 .76 1.956 80 379 .753 .908 100 2430 6080 127 137 158 168 0 1027 207 821 .988 1083 877 1.012 .946 -.018 -.08
8 1136 763 160 163 976 600 1148 771 163 167 988 608 0 0 211 168 34 46 100 100 100 100 1576 1596 1.627 .615 .615 .601 .621 1.298 52 288 .615 .875 90 2590 6080 127 136 174 183 0 991 212 779 .798 1001 790 1.252 .799 -.325 -.323
9 857 649 158 171 699 478 861 642 160 170 703 471 0 0 119 110 34 46 100 100 100 100 1177 1174 1.462 .684 .67 .675 .685 1.257 52 291 .685 .863 90 2720 6080 127 136 187 196 0 843 222 621 .888 834 612 1.126 .87 -.171 -.201
10 1134 741 158 160 976 581 1190 764 159 161 1032 604 0 0 329 206 35 47 100 100 100 98 1557 1636 1.68 .595 .585 .596 .575 1.435 80 343 .581 .882 100 2880 6080 127 137 203 213 0 962 208 755 .773 992 784 1.293 .76 -.371 -.396
11 741 477 155 163 586 314 754 495 158 165 599 332 0 0 112 118 35 42 100 96 100 96 900 931 1.866 .536 .554 .484 .549 1.691 52 300 .559 .793 90 3020 6070 126 135 217 226 0 620 212 408 .696 643 431 1.437 .72 -.523 -.474
12 949 700 154 160 795 540 988 732 158 161 834 572 0 0 142 161 36 39 100 100 100 100 1335 1406 1.472 .679 .686 .651 .688 1.32 52 313 .712 .888 90 3170 6070 126 135 232 241 0 909 208 701 .882 951 743 1.134 .891 -.181 -.167
13 1102 868 158 157 944 711 1115 883 161 161 957 726 0 0 109 123 36 42 100 100 100 100 1655 1683 1.328 .753 .759 .748 .752 1.204 52 289 .745 .9 90 3310 6080 127 136 246 255 0 1127 204 923 .978 1147 943 1.022 .985 -.032 -.021
14 1370 1078 163 162 1207 916 1363 1095 165 165 1200 933 0 0 145 136 33 45 100 100 100 100 2123 2133 1.318 .759 .778 .756 .769 1.144 52 312 .759 .944 90 3460 6070 126 135 261 270 0 1400 210 1190 .986 1422 1212 1.015 1.01 -.021 .014
15 744 610 154 158 590 452 745 594 157 163 591 436 0 0 96 90 33 48 100 100 100 100 1042 1027 1.305 .766 .738 .763 .74 1.281 52 312 .789 .861 90 3610 6070 126 135 276 285 0 792 205 587 .995 771 566 1.005 .958 -.007 -.062
16 3402 2683 149 162 3253 2521 3487 2757 153 164 3338 2595 0 0 557 640 34 47 100 100 100 100 5774 5933 1.29 .775 .777 .758 .767 1.179 52 300 .797 .955 90 3760 6070 126 135 291 300 0 3485 210 3274 1.007 3581 3370 .994 1.01 .009 .014
17 1336 961 152 161 1184 800 1367 963 153 162 1215 802 0 0 176 192 34 45 100 100 100 100 1984 2017 1.48 .676 .66 .661 .67 1.233 52 288 .708 .899 90 3900 6070 126 135 305 314 0 1248 209 1039 .878 1251 1042 1.14 .857 -.188 -.222
18 1377 1051 154 160 1223 891 1385 1058 158 164 1231 898 0 0 206 189 34 46 100 100 100 100 2114 2129 1.373 .729 .729 .718 .716 1.254 52 301 .733 .914 90 4040 6070 126 135 319 328 0 1365 208 1157 .946 1374 1166 1.057 .947 -.08 -.078
19 3390 3021 156 167 3234 2854 3599 3016 161 167 3443 2849 0 0 1094 907 35 44 100 100 100 100 6088 6292 1.133 .882 .827 .939 .869 1.471 80 383 .866 .948 110 4200 6080 126 137 334 345 0 3924 217 3707 1.146 3917 3700 .872 1.075 .197 .104
20 1113 772 158 162 955 610 1160 800 161 162 1002 638 0 0 243 211 35 43 100 98 100 97 1565 1640 1.566 .639 .637 .611 .645 1.36 80 344 .654 .895 100 4340 6070 126 136 349 359 0 1003 210 792 .83 1039 829 1.205 .827 -.27 -.274

Total number of rows: 41664

Table truncated, full table size 9479 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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