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Sample GSM148696 Query DataSets for GSM148696
Status Public on Oct 03, 2007
Title PT181_4 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47169.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT181_4 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT181_4 DNA
Prostate genomic DNA; LabeledExtract: 47169.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 = 1120, 5530; 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 = 39.28; Parameter Scan Time = 12:04:14; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135363; 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 = 39.28; Parameter Scan Time = 12:04:14; Parameter PMT Volts = 690; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500428; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; 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/2003-12/47169.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
1 602 613 129 151 473 462 624 619 139 212 495 468 0 0 154 144 63 645 100 7 96 0 935 963 1.024 .977 .945 .985 .986 1.603 52 332 3.243 .165 90 1830 6370 79 88 66 75 0 755 186 569 1.203 762 576 .831 1.165 .267 .22
2 863 749 128 138 735 611 935 803 136 155 807 665 0 0 284 219 73 184 96 98 92 76 1346 1472 1.203 .831 .824 .897 .819 1.947 52 244 .948 .523 80 1970 6370 80 88 81 89 0 923 170 753 1.024 989 819 .977 1.015 .034 .022
3 1639 1546 125 135 1514 1411 1739 1570 133 146 1614 1435 0 0 375 304 67 165 100 100 100 100 2925 3049 1.073 .932 .889 .952 .929 1.399 52 301 .953 .786 90 2110 6370 79 88 94 103 0 1904 166 1738 1.148 1934 1768 .871 1.095 .199 .131
4 706 534 127 146 579 388 732 538 133 147 605 392 0 0 281 147 49 44 94 98 88 98 967 997 1.492 .67 .648 .775 .653 2.274 52 266 .599 .678 80 2260 6370 80 88 110 118 0 658 180 478 .825 663 483 1.211 .798 -.277 -.325
5 1488 1283 125 143 1363 1140 1617 1297 126 145 1492 1154 0 0 566 463 29 48 100 100 98 97 2503 2646 1.196 .836 .773 .901 .826 2.196 80 361 .819 .84 100 2410 6370 79 89 124 134 0 1580 176 1404 1.03 1598 1421 .971 .953 .043 -.07
6 600 525 126 141 474 384 662 538 127 144 536 397 0 0 210 165 31 48 100 100 98 98 858 933 1.234 .81 .741 .862 .812 1.943 52 232 .788 .753 80 2550 6370 80 88 139 147 0 647 174 473 .998 663 489 1.002 .912 -.003 -.132
7 1264 1144 124 139 1140 1005 1309 1188 125 146 1185 1049 0 0 260 188 31 48 100 100 100 100 2145 2234 1.134 .882 .885 .9 .834 1.463 52 301 .859 .812 90 2690 6370 79 88 152 161 0 1409 171 1238 1.086 1463 1292 .921 1.09 .119 .125
8 1204 1070 127 132 1077 938 1224 1042 127 137 1097 910 0 0 212 141 30 47 100 100 100 100 2015 2007 1.148 .871 .83 .883 .84 1.329 52 300 .848 .835 90 2840 6370 79 88 167 176 0 1318 163 1155 1.073 1284 1121 .932 1.022 .101 .031
9 816 711 126 133 690 578 809 747 128 136 683 614 0 0 89 222 30 44 100 94 100 94 1268 1297 1.194 .838 .899 .786 .894 1.753 52 301 .95 .761 90 2990 6360 78 87 182 191 0 876 164 712 1.032 920 756 .969 1.107 .045 .147
10 1085 869 125 130 960 739 1227 1003 128 134 1102 873 0 0 388 346 30 44 97 97 96 96 1699 1975 1.299 .77 .792 .76 .763 2.601 80 347 .777 .842 100 3140 6370 79 89 197 207 0 1070 160 910 .948 1235 1075 1.055 .976 -.077 -.035
11 749 610 126 127 623 483 773 676 130 128 647 549 0 0 159 223 31 45 100 92 100 90 1106 1196 1.29 .775 .849 .624 .826 2.323 52 244 .842 .74 80 3290 6360 79 87 213 221 0 751 156 595 .955 833 676 1.047 1.045 -.066 .064
12 943 759 124 128 819 631 957 794 127 128 833 666 0 0 168 232 31 39 100 100 100 96 1450 1499 1.298 .77 .8 .695 .749 1.698 52 300 .81 .81 90 3430 6360 78 87 226 235 0 935 158 777 .949 978 820 1.054 .985 -.075 -.022
13 1045 958 128 138 917 820 1066 998 130 138 938 860 0 0 134 248 32 41 100 100 100 100 1737 1798 1.118 .894 .917 .837 .914 1.502 52 312 .947 .827 90 3570 6360 78 87 240 249 0 1180 170 1010 1.101 1229 1059 .908 1.129 .139 .175
14 1166 907 129 130 1037 777 1165 914 132 132 1036 784 0 0 143 145 35 43 100 100 100 100 1814 1820 1.335 .749 .757 .743 .712 1.265 52 337 .751 .793 90 3720 6360 78 87 255 264 0 1117 160 957 .923 1126 966 1.083 .932 -.116 -.101
15 634 554 128 126 506 428 627 560 130 130 499 434 0 0 107 123 28 43 100 98 100 98 934 933 1.182 .846 .87 .811 .848 1.548 52 313 .861 .763 90 3870 6360 78 87 270 279 0 682 155 527 1.042 690 535 .96 1.071 .059 .099
16 2588 2259 125 124 2463 2135 2605 2419 129 130 2480 2295 0 0 297 588 30 43 100 100 100 100 4598 4775 1.154 .867 .925 .821 .923 1.45 52 324 .912 .883 90 4020 6360 78 87 285 294 0 2783 153 2630 1.068 2980 2827 .937 1.14 .095 .189
17 1130 916 129 128 1001 788 1153 959 132 133 1024 831 0 0 194 220 32 43 100 100 100 100 1789 1855 1.27 .787 .812 .765 .806 1.432 52 288 .802 .831 90 4170 6360 78 87 300 309 0 1128 158 971 .97 1181 1024 1.031 1 -.044 -.001
18 1048 888 128 130 920 758 1061 916 129 134 933 786 0 0 132 170 30 44 100 100 100 100 1678 1719 1.214 .824 .842 .804 .836 1.358 52 300 .848 .856 90 4310 6360 78 87 314 323 0 1094 160 934 1.015 1128 968 .985 1.038 .021 .053
19 2293 1672 124 122 2169 1550 2176 1404 125 128 2052 1282 0 0 1074 920 29 42 100 100 100 100 3719 3334 1.399 .715 .625 .714 .666 2.151 80 364 .725 .782 100 4460 6360 78 88 329 339 0 2060 150 1909 .88 1729 1579 1.136 .77 -.184 -.378
20 1371 718 126 117 1245 601 1273 728 129 122 1147 611 0 0 310 168 30 40 100 100 100 100 1846 1758 2.072 .483 .533 .479 .479 1.331 52 294 .462 .826 90 4600 6360 78 87 343 352 0 884 144 740 .595 897 753 1.682 .656 -.75 -.608

Total number of rows: 41664

Table truncated, full table size 9387 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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