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Sample GSM148714 Query DataSets for GSM148714
Status Public on Oct 03, 2007
Title PT308_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47173.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT308_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT308_2 DNA
Prostate genomic DNA; LabeledExtract: 47173.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 = 38.27; Parameter Scan Time = 10:01:59; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136010; 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 = 38.27; Parameter Scan Time = 10:01:59; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501075; 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/2003-12/47173.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
1 995 1118 159 241 836 877 1021 1177 160 243 862 936 0 0 196 189 38 47 100 100 100 100 1713 1798 .953 1.049 1.086 1.057 1.053 1.192 52 286 1.046 .94 80 1580 6060 70 78 66 74 0 1028 221 806 .964 1082 860 1.037 .998 -.053 -.003
2 1191 1224 159 242 1032 982 1263 1327 162 246 1104 1085 0 0 439 416 37 49 100 100 98 100 2014 2189 1.051 .952 .983 .973 .956 1.681 52 257 .948 .911 80 1720 6060 70 78 80 88 0 1125 222 903 .875 1220 997 1.143 .903 -.193 -.147
3 1818 1845 154 236 1664 1609 1870 1854 161 237 1716 1618 0 0 306 186 37 48 100 100 100 100 3273 3334 1.034 .967 .943 .979 .941 1.221 52 315 .952 .937 90 1860 6060 69 78 93 102 0 1696 217 1479 .889 1704 1487 1.125 .867 -.17 -.207
4 1130 895 152 249 978 646 1131 921 158 246 979 672 0 0 166 182 39 51 100 100 100 96 1624 1651 1.514 .661 .686 .631 .665 1.434 32 225 .692 .846 70 2010 6050 69 76 109 116 0 823 229 594 .607 846 618 1.647 .631 -.72 -.665
5 1920 1734 155 241 1765 1493 1914 1759 160 245 1759 1518 0 0 337 344 40 51 100 100 100 100 3258 3277 1.182 .846 .863 .831 .85 1.2 52 330 .847 .943 90 2160 6050 68 77 123 132 0 1594 221 1372 .777 1617 1395 1.286 .793 -.363 -.334
6 937 992 159 241 778 751 942 1027 164 244 783 786 0 0 151 174 42 54 100 100 100 100 1529 1569 1.036 .965 1.004 .955 .987 1.216 32 201 .915 .838 70 2290 6060 70 77 137 144 0 912 221 690 .887 944 722 1.127 .923 -.173 -.116
7 1516 1702 165 243 1351 1459 1561 1721 166 245 1396 1478 0 0 337 245 37 49 100 100 100 100 2810 2874 .926 1.08 1.059 1.112 1.081 1.363 52 325 1.023 .913 90 2440 6060 69 78 151 160 0 1564 223 1341 .993 1582 1358 1.008 .973 -.011 -.039
8 1353 1396 161 236 1192 1160 1379 1451 162 242 1218 1215 0 0 213 287 36 54 100 100 100 100 2352 2433 1.028 .973 .998 .949 .978 1.256 52 314 .992 .927 90 2590 6050 68 77 166 175 0 1283 217 1066 .894 1334 1117 1.118 .917 -.161 -.125
9 967 1109 164 240 803 869 982 1096 164 240 818 856 0 0 122 173 43 49 100 100 100 100 1672 1674 .924 1.082 1.046 1.072 1.042 1.204 52 312 1.088 .899 90 2740 6050 68 77 181 190 0 1019 221 799 .995 1007 787 1.005 .962 -.008 -.056
10 1669 1008 164 245 1505 763 1518 981 169 248 1354 736 0 0 541 179 51 57 100 100 100 100 2268 2090 1.972 .507 .544 .523 .525 1.293 52 303 .474 .883 90 2880 6050 68 77 195 204 0 926 225 701 .466 902 676 2.146 .5 -1.102 -1.001
11 924 991 158 245 766 746 922 1009 163 248 764 764 0 0 167 182 49 60 100 100 100 100 1512 1528 1.027 .974 1 .968 .991 1.256 52 321 .985 .895 90 3030 6050 68 77 210 219 0 911 225 686 .895 927 702 1.117 .919 -.16 -.122
12 1061 1103 153 239 908 864 1106 1116 155 241 953 877 0 0 179 153 36 51 100 100 100 100 1772 1830 1.051 .952 .92 .96 .95 1.287 52 336 .957 .892 90 3180 6050 68 77 225 234 0 1014 220 794 .875 1026 806 1.143 .846 -.193 -.242
13 1299 1546 156 241 1143 1305 1296 1544 157 245 1140 1303 0 0 164 178 33 53 100 100 100 100 2448 2443 .876 1.142 1.143 1.143 1.139 1.175 52 300 1.14 .927 90 3330 6050 68 77 240 249 0 1421 221 1199 1.049 1419 1198 .953 1.05 .069 .071
14 1344 1520 156 236 1188 1284 1453 1588 159 240 1297 1352 0 0 375 399 36 53 100 100 98 100 2472 2649 .925 1.081 1.042 1.099 1.082 1.399 80 378 1.078 .936 100 3480 6050 68 78 255 265 0 1397 217 1180 .993 1460 1243 1.007 .958 -.01 -.062
15 853 1030 154 232 699 798 881 1026 159 238 727 794 0 0 153 141 40 51 100 100 100 100 1497 1521 .876 1.142 1.092 1.156 1.127 1.228 52 288 1.115 .889 90 3620 6050 68 77 269 278 0 947 213 733 1.049 943 730 .953 1.004 .069 .005
16 3900 4592 154 234 3746 4358 4094 4853 159 239 3940 4619 0 0 987 998 38 48 100 100 100 100 8104 8559 .86 1.163 1.172 1.178 1.163 1.171 52 316 1.153 .969 90 3770 6050 68 77 284 293 0 4220 215 4005 1.069 4460 4245 .935 1.077 .097 .108
17 1449 1825 153 233 1296 1592 1574 1892 157 236 1421 1659 0 0 406 387 37 51 100 100 100 100 2888 3080 .814 1.228 1.167 1.292 1.236 1.391 52 254 1.182 .934 80 3910 6050 69 77 299 307 0 1677 214 1463 1.129 1739 1525 .886 1.073 .175 .102
18 1485 1550 157 234 1328 1316 1530 1534 161 243 1373 1300 0 0 240 196 37 53 100 100 100 100 2644 2673 1.009 .991 .947 .998 1.003 1.167 52 300 .969 .938 90 4060 6050 68 77 313 322 0 1425 215 1210 .911 1410 1195 1.098 .87 -.135 -.201
19 3444 3929 156 231 3288 3698 3414 4131 161 235 3258 3900 0 0 1309 1252 35 54 100 100 100 100 6986 7158 .889 1.125 1.197 1.181 1.116 1.405 80 375 1.097 .955 100 4210 6050 68 78 328 338 0 3611 212 3399 1.034 3797 3584 .967 1.1 .048 .138
20 1517 880 153 227 1364 653 1493 881 159 230 1340 654 0 0 489 206 65 51 100 100 98 100 2017 1994 2.089 .479 .488 .487 .472 1.319 80 373 .455 .897 100 4370 6050 68 78 344 354 0 809 209 600 .44 810 601 2.273 .449 -1.184 -1.157

Total number of rows: 41664

Table truncated, full table size 9738 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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