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Sample GSM148703 Query DataSets for GSM148703
Status Public on Oct 03, 2007
Title PT215_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49672.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT215_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT215_2 DNA
Prostate genomic DNA; LabeledExtract: 49672.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 = 1000, 5320; 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 = 38.33; Parameter Scan Time = 09:12:41; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148604; 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 = 38.33; Parameter Scan Time = 09:12:41; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513508; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.13; 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/2004-02/49672.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 1157 1110 209 250 948 860 1193 1157 212 252 984 907 0 0 270 386 49 61 100 100 100 98 1808 1891 1.102 .907 .922 .826 .889 1.543 52 278 .966 .859 80 1620 5980 62 70 58 66 0 814 183 630 .665 848 665 1.504 .676 -.589 -.566
2 1596 358 205 258 1391 100 1711 346 214 265 1506 88 0 0 388 96 66 61 100 62 100 31 1491 1594 13.91 .072 .058 .07 .074 2.27 32 219 .044 .114 70 1760 5980 62 69 72 79 0 262 189 73 .053 254 64 18.979 .043 -4.246 -4.545
3 1962 2591 193 246 1769 2345 2000 2762 202 257 1807 2516 0 0 570 815 53 64 100 100 100 100 4114 4323 .754 1.326 1.392 1.302 1.293 1.176 52 339 1.343 .965 90 1910 5990 62 71 86 95 0 1899 180 1719 .972 2024 1844 1.029 1.021 -.042 .029
4 1688 995 197 246 1491 749 1748 953 201 255 1551 707 0 0 335 301 52 63 100 100 100 100 2240 2258 1.991 .502 .456 .465 .476 1.368 32 226 .514 .858 70 2060 5990 63 70 102 109 0 729 180 549 .368 698 518 2.716 .334 -1.441 -1.582
5 2220 2442 190 257 2030 2185 2254 2585 194 260 2064 2328 0 0 459 619 41 61 100 100 100 100 4215 4392 .929 1.076 1.128 1.053 1.098 1.211 52 349 1.109 .956 90 2220 5980 61 70 117 126 0 1790 188 1601 .789 1895 1706 1.268 .827 -.342 -.275
6 1370 1091 193 258 1177 833 1455 1141 198 265 1262 883 0 0 321 287 45 61 100 100 100 100 2010 2145 1.413 .708 .7 .68 .719 1.376 32 213 .693 .866 70 2360 5980 62 69 132 139 0 800 189 611 .519 836 647 1.928 .513 -.947 -.963
7 1698 2311 193 247 1505 2064 1790 2441 193 250 1597 2194 0 0 450 583 43 55 100 100 100 100 3569 3791 .729 1.371 1.374 1.375 1.395 1.151 52 279 1.354 .967 80 2510 5980 62 70 147 155 0 1694 181 1513 1.005 1789 1608 .995 1.007 .007 .01
8 1624 2136 188 254 1436 1882 1675 2170 193 258 1487 1916 0 0 350 601 37 64 100 100 100 100 3318 3403 .763 1.311 1.289 1.273 1.332 1.283 52 245 1.355 .94 80 2660 5980 62 70 162 170 0 1566 186 1379 .961 1590 1404 1.041 .944 -.058 -.083
9 1240 1745 191 244 1049 1501 1264 1756 196 245 1073 1512 0 0 269 369 42 65 100 100 100 100 2550 2585 .699 1.431 1.409 1.43 1.444 1.209 52 310 1.425 .94 90 2790 5980 61 70 174 183 0 1279 179 1100 1.049 1287 1108 .954 1.033 .069 .047
10 2100 1892 194 252 1906 1640 2092 1921 197 257 1898 1669 0 0 312 280 42 65 100 100 100 100 3546 3567 1.162 .86 .879 .86 .85 1.148 52 323 .849 .958 90 2950 5980 61 70 190 199 0 1387 185 1202 .631 1408 1223 1.586 .645 -.665 -.634
11 1115 1380 189 252 926 1128 1135 1446 191 250 946 1194 0 0 238 341 41 59 100 100 100 100 2054 2140 .821 1.218 1.262 1.19 1.247 1.335 52 253 1.251 .902 80 3100 5980 62 70 206 214 0 1011 185 827 .893 1060 875 1.12 .925 -.164 -.112
12 1290 1654 183 232 1107 1422 1342 1747 185 240 1159 1515 0 0 361 464 39 60 100 100 100 100 2529 2674 .778 1.285 1.307 1.276 1.262 1.249 52 245 1.28 .944 80 3230 5980 62 70 219 227 0 1212 170 1042 .941 1280 1110 1.062 .958 -.087 -.062
13 1408 2206 183 242 1225 1964 1508 2327 186 252 1325 2085 0 0 347 501 42 66 100 100 100 100 3189 3410 .624 1.603 1.574 1.642 1.592 1.261 52 322 1.572 .946 90 3370 5980 61 70 232 241 0 1617 177 1439 1.175 1706 1528 .851 1.153 .233 .206
14 1699 2608 188 245 1511 2363 1727 2666 190 252 1539 2421 0 0 378 524 41 61 100 100 100 100 3874 3960 .639 1.564 1.573 1.588 1.566 1.187 52 338 1.521 .962 90 3530 5980 61 70 248 257 0 1911 180 1732 1.146 1954 1774 .872 1.153 .197 .205
15 1104 1400 188 245 916 1155 1140 1431 190 248 952 1186 0 0 205 347 40 62 100 100 100 100 2071 2138 .793 1.261 1.246 1.226 1.245 1.274 52 272 1.301 .939 80 3690 5980 62 70 265 273 0 1026 180 847 .924 1049 869 1.082 .913 -.114 -.131
16 3246 5413 185 234 3061 5179 3314 5610 187 241 3129 5376 0 0 1012 1623 42 57 100 100 100 100 8240 8505 .591 1.692 1.718 1.711 1.645 1.195 52 243 1.683 .978 80 3830 5980 62 70 279 287 0 3967 172 3796 1.24 4112 3940 .806 1.259 .31 .333
17 1409 2051 180 232 1229 1819 1375 2069 183 238 1195 1837 0 0 415 707 41 62 100 100 100 100 3048 3032 .676 1.48 1.537 1.44 1.476 1.267 52 236 1.518 .952 80 3970 5980 62 70 293 301 0 1503 170 1333 1.085 1516 1346 .922 1.127 .117 .172
18 1805 2522 177 241 1628 2281 1785 2591 182 247 1608 2350 0 0 361 541 38 56 100 100 100 100 3909 3958 .714 1.401 1.461 1.388 1.393 1.211 52 287 1.426 .947 90 4110 5980 61 70 306 315 0 1848 177 1672 1.027 1899 1722 .974 1.071 .038 .099
19 3986 5402 177 241 3809 5161 4070 5488 182 246 3893 5247 0 0 959 1501 39 57 100 100 100 100 8970 9140 .738 1.355 1.348 1.33 1.374 1.167 52 302 1.38 .975 90 4250 5970 60 69 320 329 0 3959 177 3783 .993 4022 3846 1.007 .988 -.01 -.018
20 1634 1793 182 234 1452 1559 1657 1870 186 241 1475 1636 0 0 417 385 41 59 100 100 100 100 3011 3111 .931 1.074 1.109 1.093 1.102 1.235 52 318 1.052 .951 90 4390 5980 61 70 334 343 0 1314 172 1143 .787 1371 1199 1.271 .813 -.346 -.299

Total number of rows: 41664

Table truncated, full table size 9732 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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