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Sample GSM148749 Query DataSets for GSM148749
Status Public on Oct 03, 2007
Title PL133_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47158.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL133_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL133_1 DNA
Prostate genomic DNA; LabeledExtract: 47158.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 = 880, 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 = 39.07; Parameter Scan Time = 12:08:24; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 134299; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; 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 = 39.07; Parameter Scan Time = 12:08:24; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 499364; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; 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/2003-11/47158.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 1047 927 163 244 884 683 1059 938 165 244 896 694 0 0 180 207 38 49 100 100 100 100 1567 1590 1.294 .773 .775 .747 .758 1.252 52 332 .766 .902 90 1810 5790 66 75 88 97 0 917 241 675 .764 927 686 1.309 .766 -.388 -.385
2 1477 957 165 239 1312 718 1569 1004 166 239 1404 765 0 0 313 209 37 47 100 100 100 100 2030 2169 1.827 .547 .545 .535 .536 1.288 52 304 .537 .913 90 1940 5790 66 75 101 110 0 946 236 710 .541 993 756 1.848 .539 -.886 -.892
3 1685 1704 166 244 1519 1460 1692 1711 168 248 1526 1467 0 0 222 254 38 54 100 100 100 100 2979 2993 1.04 .961 .961 .954 .975 1.162 52 314 .956 .945 90 2090 5790 66 75 116 125 0 1685 241 1444 .95 1692 1450 1.052 .951 -.073 -.073
4 1302 710 164 248 1138 462 1342 720 165 251 1178 472 0 0 323 166 36 51 100 100 100 98 1600 1650 2.463 .406 .401 .395 .397 1.328 52 264 .397 .865 80 2240 5790 67 75 132 140 0 702 245 457 .401 712 467 2.491 .396 -1.317 -1.336
5 1748 1515 161 234 1587 1281 1713 1572 162 234 1552 1338 0 0 280 304 37 49 100 100 100 100 2868 2890 1.239 .807 .862 .788 .842 1.293 80 408 .824 .924 110 2390 5790 65 76 145 156 0 1498 231 1267 .798 1554 1323 1.253 .852 -.325 -.23
6 1198 765 159 233 1039 532 1230 776 163 236 1071 543 0 0 206 176 41 46 100 100 100 100 1571 1614 1.953 .512 .507 .49 .494 1.357 52 232 .512 .86 80 2530 5790 67 75 161 169 0 756 230 526 .506 767 537 1.975 .501 -.982 -.996
7 1527 1641 157 236 1370 1405 1551 1638 161 241 1394 1402 0 0 207 241 37 48 100 100 100 100 2775 2796 .975 1.026 1.006 1.022 1.034 1.169 52 290 1.022 .932 90 2670 5790 66 75 174 183 0 1623 233 1389 1.014 1620 1386 .986 .994 .02 -.008
8 1238 1266 158 226 1080 1040 1271 1297 161 231 1113 1071 0 0 215 265 35 48 100 100 100 100 2120 2184 1.038 .963 .962 .944 .945 1.274 80 353 .974 .929 100 2820 5790 66 76 189 199 0 1252 223 1028 .952 1282 1059 1.05 .951 -.071 -.072
9 991 1020 157 231 834 789 977 1029 157 236 820 798 0 0 141 168 37 50 100 100 100 100 1623 1618 1.057 .946 .973 .935 .942 1.229 52 302 .936 .894 90 2970 5780 65 74 204 213 0 1009 228 780 .935 1017 789 1.069 .962 -.096 -.056
10 1526 1365 159 237 1367 1128 1558 1412 160 239 1399 1175 0 0 286 285 36 50 100 100 100 100 2495 2574 1.212 .825 .84 .816 .819 1.311 80 341 .823 .928 100 3120 5790 66 76 219 229 0 1350 234 1115 .816 1396 1162 1.226 .83 -.294 -.268
11 908 915 155 232 753 683 938 964 159 231 783 732 0 0 167 181 33 48 100 100 100 100 1436 1515 1.102 .907 .935 .893 .923 1.429 52 300 .95 .889 90 3260 5780 65 74 233 242 0 905 229 675 .897 953 724 1.115 .924 -.157 -.113
12 1196 1121 154 235 1042 886 1212 1162 158 234 1058 927 0 0 193 217 36 47 100 100 100 100 1928 1985 1.176 .85 .876 .839 .87 1.32 52 313 .857 .907 90 3410 5780 65 74 248 257 0 1108 232 876 .841 1149 917 1.189 .866 -.25 -.207
13 1275 1510 157 234 1118 1276 1349 1567 160 238 1192 1333 0 0 335 379 35 47 100 100 100 100 2394 2525 .876 1.141 1.118 1.164 1.136 1.295 80 360 1.142 .938 100 3560 5790 66 76 263 273 0 1493 231 1262 1.128 1549 1318 .886 1.106 .174 .145
14 1472 1614 156 223 1316 1391 1547 1621 160 227 1391 1398 0 0 271 266 38 48 100 100 100 100 2707 2789 .946 1.057 1.005 1.071 1.05 1.29 80 346 1.057 .942 100 3710 5790 66 76 278 288 0 1596 220 1375 1.045 1603 1382 .957 .994 .064 -.009
15 862 1229 154 234 708 995 860 1300 159 237 706 1066 0 0 156 200 38 51 100 100 100 100 1703 1772 .712 1.405 1.51 1.415 1.418 1.304 52 275 1.426 .888 90 3840 5780 65 74 291 300 0 1215 231 984 1.39 1285 1054 .72 1.493 .475 .578
16 3465 4164 157 233 3308 3931 3668 4289 159 238 3511 4056 0 0 862 1024 41 54 100 100 100 100 7239 7567 .842 1.188 1.155 1.19 1.197 1.207 52 324 1.189 .967 90 3990 5780 65 74 306 315 0 4117 230 3887 1.175 4241 4010 .851 1.142 .233 .192
17 1663 1752 159 235 1504 1517 1669 1817 162 238 1510 1582 0 0 282 266 40 51 100 100 100 100 3021 3092 .991 1.009 1.048 1.013 1.013 1.184 52 313 .986 .949 90 4140 5780 65 74 321 330 0 1732 232 1500 .997 1797 1564 1.003 1.036 -.004 .051
18 1723 1816 159 245 1564 1571 1734 1792 165 247 1575 1547 0 0 204 222 41 46 100 100 100 100 3135 3122 .996 1.004 .982 1.003 1 1.155 52 300 1.009 .953 90 4290 5780 65 74 336 345 0 1796 242 1553 .993 1772 1530 1.007 .971 -.01 -.042
19 3619 4348 159 221 3460 4127 3706 4582 162 227 3547 4361 0 0 574 965 37 51 100 100 100 100 7587 7908 .838 1.193 1.229 1.157 1.227 1.335 80 359 1.213 .93 100 4440 5780 65 75 351 361 0 4299 219 4081 1.179 4530 4312 .848 1.216 .238 .282
20 1197 1010 157 218 1040 792 1275 1032 159 224 1118 814 0 0 271 183 33 48 100 100 100 100 1832 1932 1.313 .762 .728 .783 .764 1.359 80 347 .73 .91 100 4590 5790 66 76 366 376 0 999 216 783 .753 1020 805 1.328 .72 -.409 -.474

Total number of rows: 41664

Table truncated, full table size 9603 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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