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Sample GSM148735 Query DataSets for GSM148735
Status Public on Oct 03, 2007
Title PT37_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47186.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT37_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT37_1 DNA
Prostate genomic DNA; LabeledExtract: 47186.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 = 38.98; Parameter Scan Time = 09:40:18; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136784; 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 = 38.98; Parameter Scan Time = 09:40:18; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501850; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; 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/2003-12/47186.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
1 827 809 158 219 669 590 860 816 161 222 702 597 0 0 232 239 34 52 100 98 100 94 1259 1299 1.134 .882 .85 .823 .895 1.619 52 298 .915 .859 80 1670 5520 40 48 95 103 0 915 248 667 .997 922 675 1.003 .961 -.004 -.057
2 1356 1141 158 221 1198 920 1419 1205 163 229 1261 984 0 0 228 320 37 64 100 100 100 100 2118 2245 1.302 .768 .78 .725 .751 1.392 32 210 .81 .87 70 1820 5520 40 47 110 117 0 1290 250 1040 .868 1362 1112 1.152 .882 -.204 -.181
3 1992 1772 157 212 1835 1560 2217 1886 159 218 2060 1674 0 0 608 476 33 61 100 100 100 100 3395 3734 1.176 .85 .813 .867 .879 1.292 52 335 .827 .939 90 1950 5530 40 49 122 131 0 2003 240 1764 .961 2132 1892 1.04 .919 -.057 -.122
4 1117 745 156 231 961 514 1119 745 162 231 963 514 0 0 205 189 39 59 100 100 100 96 1475 1477 1.87 .535 .534 .505 .491 1.349 32 146 .55 .858 60 2120 5520 41 47 141 147 0 842 261 581 .605 842 581 1.654 .603 -.726 -.729
5 2226 1963 156 219 2070 1744 2293 2063 160 223 2137 1844 0 0 554 595 39 59 100 100 100 100 3814 3981 1.187 .843 .863 .819 .828 1.22 52 335 .848 .944 90 2230 5520 39 48 150 159 0 2219 248 1972 .952 2332 2085 1.05 .975 -.07 -.036
6 881 781 155 221 726 560 898 755 159 226 743 534 0 0 172 187 38 57 100 100 100 100 1286 1277 1.296 .771 .719 .755 .736 1.455 32 170 .778 .813 60 2410 5520 41 47 170 176 0 883 250 633 .872 854 604 1.147 .812 -.198 -.3
7 1900 1906 156 219 1744 1687 1980 1951 159 221 1824 1732 0 0 460 435 35 55 100 100 100 100 3431 3556 1.034 .967 .95 .98 .96 1.307 52 328 .974 .93 90 2550 5520 39 48 182 191 0 2155 248 1907 1.094 2206 1958 .914 1.073 .129 .102
8 1755 1774 161 214 1594 1560 1809 1797 165 221 1648 1583 0 0 273 263 36 54 100 100 100 100 3154 3231 1.022 .979 .961 .98 .986 1.181 52 309 .967 .954 90 2700 5530 40 49 197 206 0 2006 242 1764 1.106 2032 1790 .904 1.086 .146 .119
9 1134 1315 161 217 973 1098 1137 1353 163 224 976 1136 0 0 183 213 33 57 100 100 100 100 2071 2112 .886 1.128 1.164 1.127 1.136 1.192 52 242 1.135 .927 80 2850 5520 40 48 213 221 0 1487 245 1241 1.276 1530 1284 .784 1.316 .351 .396
10 1761 1582 160 220 1601 1362 1787 1620 163 221 1627 1400 0 0 273 337 33 61 100 100 100 100 2963 3027 1.175 .851 .86 .836 .853 1.225 52 300 .857 .926 90 2980 5520 39 48 225 234 0 1788 249 1540 .962 1831 1583 1.04 .973 -.056 -.04
11 945 992 159 208 786 784 964 1003 163 215 805 795 0 0 204 230 34 53 100 100 100 100 1570 1600 1.003 .997 .988 .982 .979 1.285 52 292 1.008 .908 80 3140 5520 40 48 242 250 0 1121 235 886 1.128 1134 899 .887 1.116 .173 .159
12 1269 1212 158 204 1111 1008 1280 1189 161 211 1122 985 0 0 225 234 37 54 100 100 100 100 2119 2107 1.102 .907 .878 .902 .928 1.283 52 275 .907 .902 80 3290 5520 40 48 257 265 0 1370 231 1140 1.026 1344 1114 .975 .992 .037 -.011
13 1560 1748 160 203 1400 1545 1629 1779 163 208 1469 1576 0 0 269 278 38 54 100 100 100 100 2945 3045 .906 1.104 1.073 1.11 1.104 1.199 52 277 1.099 .925 90 3430 5520 39 48 270 279 0 1976 229 1747 1.248 2011 1782 .802 1.213 .319 .278
14 1666 1816 167 211 1499 1605 1738 1953 170 218 1571 1742 0 0 400 430 38 56 100 100 100 100 3104 3313 .934 1.071 1.109 1.074 1.108 1.245 52 328 1.065 .935 90 3560 5510 38 47 283 292 0 2053 239 1814 1.21 2208 1969 .826 1.254 .276 .326
15 1026 1164 163 211 863 953 1044 1194 168 220 881 983 0 0 145 230 48 66 100 100 100 100 1816 1864 .906 1.104 1.116 1.081 1.134 1.283 52 321 1.128 .905 90 3730 5520 39 48 300 309 0 1316 239 1077 1.248 1350 1111 .801 1.261 .32 .335
16 3991 4200 159 209 3832 3991 4102 4240 159 212 3943 4031 0 0 881 853 34 50 100 100 100 100 7823 7974 .96 1.041 1.022 1.05 1.02 1.19 52 316 1.031 .973 90 3870 5520 39 48 314 323 0 4748 236 4512 1.177 4793 4557 .849 1.156 .236 .209
17 1549 1718 160 212 1389 1506 1628 1743 163 216 1468 1531 0 0 355 283 38 51 100 100 100 100 2895 2999 .922 1.084 1.043 1.118 1.073 1.255 52 264 1.055 .941 80 4020 5520 40 48 330 338 0 1942 240 1703 1.226 1970 1731 .816 1.179 .294 .238
18 1896 1958 163 216 1733 1742 1887 1990 169 220 1724 1774 0 0 227 293 38 57 100 100 100 100 3475 3498 .995 1.005 1.029 .998 1.015 1.15 52 255 1.013 .956 80 4170 5520 40 48 345 353 0 2214 244 1969 1.136 2250 2006 .88 1.163 .184 .218
19 3698 3236 161 217 3537 3019 3050 2726 164 222 2889 2509 0 0 1678 1397 37 59 100 100 100 100 6556 5398 1.172 .854 .868 .851 .832 1.17 52 303 .844 .95 90 4310 5510 38 47 358 367 0 3658 245 3413 .965 3082 2836 1.036 .982 -.051 -.026
20 1550 1292 157 212 1393 1080 1551 1312 162 218 1394 1100 0 0 165 191 39 58 100 100 100 100 2473 2494 1.29 .775 .789 .768 .767 1.202 52 317 .784 .929 90 4450 5510 38 47 372 381 0 1461 240 1221 .876 1483 1244 1.141 .892 -.19 -.165

Total number of rows: 41664

Table truncated, full table size 9468 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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