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Sample GSM148718 Query DataSets for GSM148718
Status Public on Oct 03, 2007
Title PT312_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47176.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT312_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT312_2 DNA
Prostate genomic DNA; LabeledExtract: 47176.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, 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 = 38.76; Parameter Scan Time = 10:46:42; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136054; 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 = 38.76; Parameter Scan Time = 10:46:42; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501119; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; 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/2003-12/47176.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
1 854 1005 146 228 708 777 869 1032 151 233 723 804 0 0 164 233 37 49 100 100 100 100 1485 1527 .911 1.097 1.112 1.065 1.06 1.424 52 300 1.146 .868 80 1670 6020 66 74 75 83 0 1024 232 791 1.118 1051 819 .895 1.133 .161 .18
2 1429 1253 151 231 1278 1022 1442 1295 153 238 1291 1064 0 0 214 194 37 54 100 100 100 100 2300 2355 1.25 .8 .824 .792 .819 1.188 32 210 .808 .878 70 1800 6020 66 73 88 95 0 1276 235 1041 .815 1319 1084 1.228 .839 -.296 -.252
3 1668 1524 150 233 1518 1291 1717 1584 175 242 1567 1351 0 0 273 311 298 72 100 100 100 100 2809 2918 1.176 .85 .862 .832 .874 1.272 52 340 .87 .912 90 1950 6020 65 74 102 111 0 1552 237 1315 .866 1613 1376 1.154 .878 -.207 -.187
4 1091 894 154 243 937 651 1096 874 158 246 942 631 0 0 239 270 35 52 100 100 100 100 1588 1573 1.439 .695 .67 .673 .695 1.332 32 214 .718 .833 70 2090 6020 66 73 117 124 0 911 248 663 .708 890 643 1.413 .682 -.499 -.552
5 1714 1536 150 230 1564 1306 1637 1515 154 232 1487 1285 0 0 397 331 37 49 100 100 100 100 2870 2772 1.198 .835 .864 .832 .847 1.198 52 341 .832 .926 90 2240 6020 65 74 131 140 0 1565 234 1330 .851 1543 1309 1.176 .88 -.234 -.184
6 925 983 150 242 775 741 951 997 153 241 801 755 0 0 173 165 38 51 100 100 100 100 1516 1556 1.046 .956 .943 .956 .948 1.243 32 215 .937 .869 70 2380 6030 67 74 146 153 0 1001 247 755 .974 1016 769 1.027 .96 -.038 -.059
7 1352 1277 150 230 1202 1047 1355 1288 152 233 1205 1058 0 0 198 244 35 52 100 100 100 100 2249 2263 1.148 .871 .878 .853 .896 1.264 52 322 .901 .901 90 2540 6020 65 74 161 170 0 1301 234 1066 .887 1312 1078 1.127 .894 -.173 -.161
8 1281 1211 156 232 1125 979 1293 1219 156 232 1137 987 0 0 221 186 36 50 100 100 100 100 2104 2124 1.149 .87 .868 .869 .885 1.195 52 301 .895 .872 90 2680 6020 65 74 175 184 0 1234 236 997 .886 1242 1005 1.128 .884 -.174 -.178
9 910 986 160 245 750 741 894 994 163 245 734 749 0 0 137 137 37 46 100 100 100 100 1491 1483 1.012 .988 1.02 .986 .979 1.263 52 254 .992 .854 80 2830 6020 66 74 191 199 0 1004 250 755 1.006 1012 763 .994 1.039 .009 .056
10 1395 1331 156 234 1239 1097 1514 1416 157 236 1358 1182 0 0 408 357 36 44 100 100 100 100 2336 2540 1.129 .885 .87 .892 .898 1.323 80 346 .872 .927 100 2980 6020 65 75 205 215 0 1356 238 1117 .902 1442 1204 1.109 .887 -.149 -.174
11 907 910 158 236 749 674 935 918 159 237 777 682 0 0 134 132 36 42 100 100 100 100 1423 1459 1.111 .9 .878 .899 .891 1.277 52 251 .897 .897 80 3120 6020 66 74 220 228 0 927 240 687 .917 935 695 1.091 .894 -.126 -.162
12 1139 1107 160 243 979 864 1146 1117 165 243 986 874 0 0 171 129 35 49 100 100 100 100 1843 1860 1.133 .883 .886 .887 .882 1.214 52 266 .881 .917 80 3270 6020 66 74 235 243 0 1128 248 880 .899 1138 890 1.112 .903 -.154 -.147
13 1156 1275 157 235 999 1040 1306 1373 159 234 1149 1138 0 0 410 417 37 52 98 100 96 98 2039 2287 .961 1.041 .99 1.119 1.055 1.792 80 364 1.036 .92 100 3420 6020 65 75 249 259 0 1299 239 1059 1.06 1399 1159 .943 1.009 .085 .013
14 1265 1417 156 235 1109 1182 1363 1515 157 237 1207 1280 0 0 339 349 38 49 100 100 100 100 2291 2487 .938 1.066 1.06 1.067 1.04 1.443 80 357 1.054 .908 100 3570 6020 65 75 264 274 0 1443 239 1204 1.086 1543 1304 .921 1.08 .119 .111
15 885 926 160 233 725 693 898 947 163 234 738 714 0 0 134 127 35 49 100 100 100 100 1418 1452 1.046 .956 .967 .956 .948 1.235 52 276 .959 .893 90 3710 6020 65 74 278 287 0 943 237 706 .974 965 727 1.027 .985 -.039 -.021
16 3220 3614 154 224 3066 3390 3370 3740 157 227 3216 3516 0 0 624 632 56 52 100 100 100 100 6456 6732 .904 1.106 1.093 1.11 1.1 1.117 52 328 1.098 .967 90 3860 6020 65 74 293 302 0 3681 228 3453 1.126 3810 3581 .888 1.114 .172 .155
17 1409 1613 144 217 1265 1396 1424 1654 149 219 1280 1437 0 0 263 266 37 45 100 100 100 100 2661 2717 .906 1.104 1.123 1.108 1.068 1.241 52 254 1.102 .917 80 4010 6020 66 74 309 317 0 1643 221 1422 1.124 1685 1464 .89 1.144 .169 .193
18 1540 1630 148 213 1392 1417 1536 1617 152 216 1388 1404 0 0 193 226 38 48 100 100 100 100 2809 2792 .982 1.018 1.012 1.014 1.029 1.155 52 300 1.015 .927 90 4150 6020 65 74 322 331 0 1660 217 1443 1.037 1647 1430 .964 1.03 .052 .043
19 3617 3711 144 209 3473 3502 3933 3869 148 211 3789 3660 0 0 1451 1312 36 44 100 100 100 100 6975 7449 .992 1.008 .966 1.052 .975 1.558 80 377 .988 .94 100 4310 6020 65 75 338 348 0 3780 213 3567 1.027 3941 3728 .974 .984 .039 -.023
20 1272 1078 144 210 1128 868 1313 1052 146 212 1169 842 0 0 139 142 33 42 100 100 100 100 1996 2011 1.3 .77 .72 .766 .745 1.188 52 300 .758 .917 90 4450 6020 65 74 352 361 0 1098 214 884 .784 1072 858 1.276 .734 -.351 -.447

Total number of rows: 41664

Table truncated, full table size 9676 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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