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Sample GSM148698 Query DataSets for GSM148698
Status Public on Oct 03, 2007
Title PT314_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48000.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT314_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT314_2 DNA
Prostate genomic DNA; LabeledExtract: 48000.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, 4960; 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 = 38.45; Parameter Scan Time = 11:24:37; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142628; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; 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 = 38.45; Parameter Scan Time = 11:24:37; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507693; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; 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/2004-01/48000.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 1284 1374 189 251 1095 1123 1324 1411 195 262 1135 1160 0 0 273 491 59 81 100 100 100 100 2218 2295 .975 1.026 1.022 .932 1.058 1.545 32 230 1.081 .877 70 1720 6070 107 114 88 95 0 1137 208 929 .848 1167 960 1.179 .845 -.237 -.242
2 1911 1830 178 255 1733 1575 2083 1871 185 252 1905 1616 0 0 449 475 39 53 100 100 100 100 3308 3521 1.1 .909 .848 .898 .94 1.259 32 172 .907 .915 60 1880 6080 109 115 105 111 0 1514 211 1303 .752 1548 1337 1.33 .702 -.412 -.511
3 2604 3393 189 252 2415 3141 2910 3588 216 294 2721 3336 0 0 794 1230 165 267 100 100 100 96 5556 6057 .769 1.301 1.226 1.232 1.314 1.346 32 226 1.361 .934 70 2010 6070 107 114 117 124 0 2807 208 2598 1.076 2968 2760 .929 1.014 .105 .02
4 1799 1414 177 229 1622 1185 1940 1506 181 235 1763 1277 0 0 431 400 39 54 100 100 100 100 2807 3040 1.369 .731 .724 .708 .667 1.309 32 206 .725 .862 70 2180 6080 108 115 134 141 0 1170 189 980 .604 1246 1056 1.655 .599 -.727 -.739
5 2719 3038 182 243 2537 2795 2689 3092 184 248 2507 2849 0 0 766 1055 39 57 100 100 100 100 5332 5356 .908 1.102 1.136 1.047 1.101 1.341 52 270 1.134 .937 80 2300 6080 108 116 146 154 0 2513 201 2312 .911 2558 2357 1.097 .94 -.134 -.089
6 1414 1345 187 247 1227 1098 1520 1471 188 245 1333 1224 0 0 413 345 40 53 100 100 100 100 2325 2557 1.117 .895 .918 .927 .904 1.472 32 220 .865 .888 70 2460 6080 108 115 162 169 0 1113 204 908 .74 1217 1012 1.351 .76 -.434 -.397
7 1963 2322 181 236 1782 2086 2101 2542 186 240 1920 2306 0 0 578 736 40 51 100 100 100 100 3868 4226 .854 1.171 1.201 1.148 1.199 1.385 52 278 1.188 .938 80 2600 6080 108 116 176 184 0 1921 195 1726 .968 2103 1907 1.033 .993 -.046 -.009
8 1979 2337 178 242 1801 2095 2082 2459 184 242 1904 2217 0 0 508 709 37 50 100 100 100 100 3896 4121 .86 1.163 1.164 1.132 1.157 1.312 52 252 1.198 .94 80 2760 6080 108 116 192 200 0 1933 200 1733 .962 2034 1834 1.039 .963 -.056 -.054
9 1718 1578 187 248 1531 1330 1782 1625 190 253 1595 1377 0 0 550 444 43 57 98 100 98 100 2861 2972 1.151 .869 .863 .949 .849 1.774 52 253 .849 .911 80 2900 6080 108 116 206 214 0 1305 205 1100 .719 1344 1139 1.392 .714 -.477 -.486
10 2230 2371 188 237 2042 2134 2304 2307 189 242 2116 2070 0 0 508 710 40 56 100 100 100 100 4176 4186 .957 1.045 .978 1.01 1.024 1.288 52 254 1.07 .935 80 3040 6080 108 116 220 228 0 1961 196 1765 .864 1908 1712 1.157 .809 -.21 -.305
11 1355 1577 183 246 1172 1331 1403 1609 186 251 1220 1363 0 0 271 221 40 55 100 100 100 100 2503 2583 .881 1.136 1.117 1.154 1.113 1.23 32 219 1.101 .907 70 3190 6080 108 115 235 242 0 1304 203 1101 .939 1331 1127 1.064 .924 -.09 -.114
12 1461 1683 189 239 1272 1444 1625 1839 194 248 1436 1600 0 0 459 485 43 57 100 100 98 100 2716 3036 .881 1.135 1.114 1.207 1.121 1.567 52 294 1.126 .944 80 3340 6080 108 116 250 258 0 1392 198 1194 .939 1521 1324 1.065 .922 -.091 -.118
13 1678 2362 188 235 1490 2127 1717 2458 189 239 1529 2223 0 0 484 549 38 52 98 100 98 100 3617 3752 .701 1.428 1.454 1.583 1.419 1.945 52 238 1.396 .93 80 3490 6080 108 116 265 273 0 1954 194 1759 1.181 2033 1839 .847 1.203 .24 .266
14 2001 2159 185 236 1816 1923 2077 2282 188 240 1892 2046 0 0 466 437 48 57 100 100 100 100 3739 3938 .944 1.059 1.081 1.095 1.069 1.335 52 264 1.036 .926 80 3620 6080 108 116 278 286 0 1786 195 1591 .876 1888 1692 1.142 .895 -.191 -.161
15 1256 1627 186 239 1070 1388 1315 1774 186 245 1129 1535 0 0 302 370 41 53 100 100 100 100 2458 2664 .771 1.297 1.36 1.31 1.262 1.327 52 262 1.29 .929 80 3780 6080 108 116 294 302 0 1346 198 1148 1.073 1467 1270 .932 1.125 .102 .169
16 4043 6097 178 235 3865 5862 4003 6511 186 246 3825 6276 0 0 1733 2556 66 89 100 100 100 100 9727 10101 .659 1.517 1.641 1.504 1.51 1.313 52 320 1.517 .963 90 3930 6080 107 116 308 317 0 5043 194 4849 1.255 5386 5191 .797 1.357 .327 .441
17 1611 2137 182 245 1429 1892 1822 2309 186 249 1640 2064 0 0 609 753 37 52 100 100 98 100 3321 3704 .755 1.324 1.259 1.409 1.3 1.562 52 256 1.314 .952 80 4080 6080 108 116 324 332 0 1768 203 1565 1.095 1910 1707 .913 1.041 .131 .058
18 1810 2313 181 249 1629 2064 1932 2511 183 249 1751 2262 0 0 482 626 36 53 100 100 100 100 3693 4013 .789 1.267 1.292 1.262 1.29 1.282 52 252 1.275 .942 80 4230 6080 108 116 339 347 0 1913 206 1707 1.048 2077 1871 .954 1.069 .068 .096
19 4549 5696 180 237 4369 5459 5004 6330 185 237 4824 6093 0 0 1145 1863 34 52 100 100 100 100 9828 10917 .8 1.249 1.263 1.135 1.289 1.711 52 283 1.297 .937 90 4370 6070 106 115 352 361 0 4712 196 4516 1.034 5236 5040 .968 1.045 .048 .063
20 1525 1613 188 238 1337 1375 1605 1643 189 239 1417 1405 0 0 309 297 42 50 100 100 100 100 2712 2822 .972 1.028 .992 1.04 1.046 1.254 52 263 1.014 .918 80 4490 6080 108 116 365 373 0 1334 197 1137 .851 1359 1162 1.176 .82 -.233 -.286

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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