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Sample GSM148721 Query DataSets for GSM148721
Status Public on Oct 03, 2007
Title PT229_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49681.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT229_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT229_1 DNA
Prostate genomic DNA; LabeledExtract: 49681.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 = 840, 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 = 38.69; Parameter Scan Time = 09:58:08; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; 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 = 38.69; Parameter Scan Time = 09:58:08; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514892; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.25; 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/2004-02/49681.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
1 683 649 163 266 520 383 709 668 166 265 546 402 0 0 144 134 35 52 100 96 100 93 903 948 1.358 .737 .736 .693 .718 1.668 32 220 .769 .762 70 1670 6120 100 107 79 86 0 665 272 392 .754 684 412 1.326 .754 -.407 -.407
2 1077 623 163 255 914 368 1093 611 165 257 930 356 0 0 193 152 36 53 100 100 100 90 1282 1286 2.484 .403 .383 .368 .392 1.605 32 176 .418 .776 60 1820 6120 101 107 95 101 0 638 261 377 .412 626 365 2.425 .392 -1.278 -1.351
3 1147 1168 158 252 989 916 1208 1176 165 255 1050 924 0 0 235 236 38 51 100 100 100 100 1905 1974 1.08 .926 .88 .902 .941 1.433 32 229 .943 .903 70 1960 6120 100 107 108 115 0 1196 258 938 .948 1204 946 1.054 .901 -.076 -.15
4 939 473 159 246 780 227 972 449 162 250 813 203 0 0 183 90 36 50 100 100 100 93 1007 1016 3.436 .291 .25 .28 .295 1.487 32 176 .278 .642 60 2110 6120 101 107 124 130 0 484 252 232 .298 460 208 3.355 .256 -1.746 -1.967
5 1192 1016 157 247 1035 769 1205 1068 162 252 1048 821 0 0 279 251 51 59 100 100 100 98 1804 1869 1.346 .743 .783 .716 .749 1.433 52 299 .758 .898 80 2260 6110 99 107 138 146 0 1040 253 788 .761 1094 841 1.314 .802 -.394 -.318
6 771 485 152 244 619 241 765 464 153 247 613 220 0 0 136 107 32 49 100 96 100 90 860 833 2.568 .389 .359 .352 .357 1.628 32 166 .394 .678 60 2410 6130 102 108 154 160 0 497 250 247 .399 475 225 2.508 .368 -1.327 -1.444
7 812 904 152 240 660 664 921 970 154 243 769 730 0 0 305 300 37 53 100 100 96 94 1324 1499 .994 1.006 .949 1.018 .982 1.515 52 278 1.001 .892 80 2550 6120 100 108 167 175 0 926 246 680 1.03 993 748 .971 .972 .043 -.041
8 862 904 151 232 711 672 933 966 155 233 782 734 0 0 246 242 38 48 100 100 100 98 1383 1516 1.058 .945 .939 .944 .939 1.416 52 275 .959 .907 80 2700 6120 100 108 182 190 0 926 238 688 .968 989 752 1.033 .961 -.047 -.057
9 730 853 157 238 573 615 739 857 161 241 582 619 0 0 146 182 36 49 100 100 100 100 1188 1201 .932 1.073 1.064 1.069 1.08 1.31 32 213 1.091 .825 70 2850 6120 100 107 197 204 0 874 244 630 1.099 878 634 .91 1.089 .136 .123
10 1035 971 150 235 885 736 1167 996 153 238 1017 761 0 0 351 280 34 52 100 100 98 100 1621 1778 1.202 .832 .748 .866 .88 1.552 52 277 .818 .895 80 2990 6120 100 108 211 219 0 994 241 754 .852 1020 779 1.174 .766 -.232 -.384
11 700 703 151 227 549 476 705 707 156 229 554 480 0 0 108 112 37 54 100 100 100 100 1025 1034 1.153 .867 .866 .86 .914 1.258 32 226 .874 .834 70 3140 6120 100 107 226 233 0 720 232 487 .888 724 492 1.126 .887 -.172 -.173
12 777 799 154 237 623 562 822 834 157 238 668 597 0 0 155 110 38 56 100 100 100 100 1185 1265 1.109 .902 .894 .919 .904 1.378 32 230 .895 .844 70 3290 6120 100 107 241 248 0 818 243 576 .924 854 611 1.082 .915 -.114 -.128
13 784 989 152 225 632 764 890 1090 155 231 738 865 0 0 278 330 31 54 96 100 96 94 1396 1603 .827 1.209 1.172 1.167 1.248 1.459 52 264 1.217 .897 80 3440 6120 100 108 256 264 0 1013 230 782 1.238 1116 886 .808 1.2 .308 .263
14 962 1119 150 226 812 893 1036 1126 152 232 886 900 0 0 284 278 33 50 100 100 100 100 1705 1786 .909 1.1 1.016 1.142 1.044 1.409 52 268 1.081 .895 80 3580 6120 100 108 270 278 0 1146 231 914 1.126 1153 922 .888 1.04 .171 .057
15 644 670 147 235 497 435 640 675 154 238 493 440 0 0 113 100 39 49 100 100 100 100 932 933 1.143 .875 .892 .876 .841 1.363 32 212 .884 .791 70 3720 6120 100 107 284 291 0 686 241 445 .896 691 451 1.116 .914 -.158 -.13
16 2132 2590 148 233 1984 2357 2296 2755 158 241 2148 2522 0 0 555 704 71 71 100 100 100 100 4341 4670 .842 1.188 1.174 1.174 1.18 1.216 32 236 1.192 .962 70 3870 6120 100 107 299 306 0 2652 239 2414 1.217 2821 2583 .822 1.202 .283 .266
17 992 1201 152 224 840 977 1004 1262 155 230 852 1038 0 0 169 255 37 49 100 100 100 100 1817 1890 .86 1.163 1.218 1.14 1.129 1.22 32 210 1.151 .931 70 4020 6120 100 107 314 321 0 1230 229 1001 1.191 1292 1063 .84 1.248 .252 .319
18 1026 999 151 232 875 767 1114 1069 154 234 963 837 0 0 342 314 37 53 100 100 100 100 1642 1800 1.141 .877 .869 .879 .902 1.339 52 274 .877 .934 80 4170 6120 100 108 329 337 0 1023 238 785 .898 1095 857 1.114 .89 -.156 -.168
19 2340 2554 152 219 2188 2335 2445 2596 154 228 2293 2377 0 0 773 745 37 55 100 100 100 100 4523 4670 .937 1.067 1.037 1.105 1.033 1.261 52 258 1.045 .955 80 4310 6120 100 108 343 351 0 2615 224 2391 1.093 2658 2434 .915 1.062 .128 .086
20 948 837 158 226 790 611 998 876 157 229 840 650 0 0 242 185 35 46 98 100 98 100 1401 1490 1.293 .773 .774 .795 .792 1.413 52 292 .768 .901 80 4460 6120 100 108 358 366 0 857 231 626 .792 897 666 1.263 .792 -.336 -.336

Total number of rows: 41664

Table truncated, full table size 9458 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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