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Sample GSM148738 Query DataSets for GSM148738
Status Public on Oct 03, 2007
Title PT265_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48742.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT265_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT265_1 DNA
Prostate genomic DNA; LabeledExtract: 48742.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 = 1080, 5200; 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 = 38.82; Parameter Scan Time = 11:07:49; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147883; 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 = 38.82; Parameter Scan Time = 11:07:49; Parameter PMT Volts = 660; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512786; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; 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/2004-01/48742.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
1 659 681 143 205 516 476 630 672 150 213 487 467 0 0 140 118 47 53 100 100 100 100 992 954 1.084 .922 .959 .929 .896 1.333 32 236 .904 .853 70 1870 6050 81 88 75 82 0 818 246 572 1.108 808 561 .902 1.152 .149 .205
2 902 786 141 223 761 563 893 806 144 221 752 583 0 0 200 196 34 53 100 100 100 100 1324 1335 1.352 .74 .775 .719 .73 1.331 32 176 .732 .825 60 2020 6060 83 89 91 97 0 944 268 677 .889 969 701 1.125 .932 -.17 -.102
3 1421 1441 147 218 1274 1223 1480 1478 156 224 1333 1260 0 0 235 254 73 75 100 100 100 100 2497 2593 1.042 .96 .945 .952 .947 1.179 32 226 .975 .935 70 2170 6050 81 88 105 112 0 1732 262 1470 1.154 1776 1514 .867 1.136 .206 .184
4 789 582 148 205 641 377 842 624 153 208 694 419 0 0 189 153 39 50 100 100 100 96 1018 1113 1.7 .588 .604 .565 .606 1.589 32 172 .556 .712 60 2300 6060 83 89 119 125 0 699 246 453 .707 750 503 1.415 .725 -.501 -.463
5 1465 1286 145 211 1320 1075 1479 1295 147 213 1334 1084 0 0 280 226 33 52 100 100 100 100 2395 2418 1.228 .814 .813 .813 .816 1.242 52 352 .806 .926 90 2460 6060 81 90 133 142 0 1545 254 1292 .979 1556 1303 1.022 .976 -.031 -.034
6 616 499 143 201 473 298 633 511 145 208 490 310 0 0 117 105 35 51 100 100 100 96 771 800 1.587 .63 .633 .604 .623 1.52 32 166 .61 .68 60 2600 6060 83 89 149 155 0 600 242 358 .757 614 373 1.321 .76 -.402 -.395
7 1112 1176 139 202 973 974 1155 1183 142 209 1016 981 0 0 265 281 34 48 100 100 100 100 1947 1997 .999 1.001 .966 1.01 .979 1.362 52 286 1.006 .929 80 2750 6060 82 90 163 171 0 1413 243 1170 1.203 1422 1179 .831 1.16 .266 .214
8 992 1070 137 215 855 855 1036 1046 141 220 899 831 0 0 313 327 35 55 100 100 100 100 1710 1730 1 1 .924 .989 .995 1.317 52 247 1.01 .922 80 2900 6060 82 90 178 186 0 1286 258 1027 1.202 1257 999 .832 1.111 .265 .152
9 817 990 147 212 670 778 842 994 151 217 695 782 0 0 209 240 42 55 100 100 100 100 1448 1477 .861 1.161 1.125 1.166 1.194 1.3 52 254 1.168 .901 80 3040 6060 82 90 192 200 0 1190 255 935 1.395 1194 940 .717 1.352 .481 .435
10 1354 1337 143 202 1211 1135 1344 1398 148 210 1201 1196 0 0 348 290 41 53 100 100 100 100 2346 2397 1.067 .937 .996 .943 .946 1.262 52 317 .926 .943 90 3190 6050 80 89 206 215 0 1607 243 1364 1.126 1680 1437 .888 1.197 .172 .259
11 834 791 148 213 686 578 845 789 151 215 697 576 0 0 163 130 36 51 100 100 100 100 1264 1273 1.187 .843 .826 .847 .889 1.316 32 220 .858 .855 70 3330 6050 81 88 221 228 0 951 256 695 1.012 948 692 .988 .993 .018 -.01
12 814 887 148 208 666 679 808 945 153 216 660 737 0 0 193 274 64 70 100 100 100 100 1345 1397 .981 1.02 1.117 .943 1.031 1.425 32 228 1.054 .907 70 3470 6040 80 87 235 242 0 1066 250 816 1.225 1136 886 .816 1.342 .293 .424
13 1020 1215 143 208 877 1007 1078 1246 145 212 935 1038 0 0 263 320 36 51 100 100 100 100 1884 1973 .871 1.148 1.11 1.138 1.145 1.282 52 289 1.149 .932 80 3620 6060 82 90 250 258 0 1460 250 1210 1.38 1497 1247 .725 1.334 .464 .416
14 1281 1538 144 215 1137 1323 1286 1550 148 218 1142 1335 0 0 152 198 36 44 100 100 100 100 2460 2477 .859 1.164 1.169 1.162 1.173 1.165 52 327 1.165 .949 90 3780 6050 80 89 265 274 0 1848 258 1590 1.398 1863 1604 .715 1.405 .484 .49
15 754 802 143 210 611 592 761 834 149 210 618 624 0 0 222 183 36 48 100 98 100 98 1203 1242 1.032 .969 1.01 .981 .985 1.494 52 254 .952 .86 80 3920 6050 81 89 280 288 0 964 252 711 1.164 1002 750 .859 1.213 .219 .279
16 2222 2695 145 205 2077 2490 2226 2633 147 208 2081 2428 0 0 721 935 35 48 100 100 100 100 4567 4509 .834 1.199 1.167 1.181 1.18 1.29 52 278 1.217 .959 80 4070 6050 81 89 295 303 0 3238 246 2992 1.441 3164 2918 .694 1.402 .527 .488
17 1011 1104 151 218 860 886 1007 1062 150 221 856 844 0 0 240 207 33 52 100 100 100 100 1746 1700 .971 1.03 .986 1.048 1.003 1.239 32 208 1.01 .907 70 4210 6050 81 88 309 316 0 1327 262 1065 1.238 1276 1014 .808 1.185 .308 .245
18 1422 1510 149 224 1273 1286 1448 1636 157 237 1299 1412 0 0 262 352 55 89 100 100 100 100 2559 2711 .99 1.01 1.087 .988 1.017 1.226 32 232 1.042 .932 70 4350 6040 80 87 323 330 0 1814 269 1545 1.214 1966 1697 .824 1.306 .28 .385
19 2484 2064 150 222 2334 1842 2392 2022 152 226 2242 1800 0 0 603 501 38 55 100 100 100 100 4176 4042 1.267 .789 .803 .785 .795 1.181 52 337 .793 .951 90 4510 6050 80 89 338 347 0 2480 267 2213 .948 2430 2163 1.054 .965 -.077 -.052
20 1353 1255 154 230 1199 1025 1326 1268 155 232 1172 1038 0 0 174 154 33 52 100 100 100 100 2224 2210 1.17 .855 .886 .854 .861 1.201 52 324 .852 .933 90 4650 6050 80 89 352 361 0 1508 276 1232 1.027 1524 1247 .973 1.064 .039 .09

Total number of rows: 41664

Table truncated, full table size 9365 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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