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Sample GSM148751 Query DataSets for GSM148751
Status Public on Oct 03, 2007
Title PT318_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49665.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT318_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT318_2 DNA
Prostate genomic DNA; LabeledExtract: 49665.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 = 38.15; Parameter Scan Time = 09:59:07; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148292; 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 = 38.15; Parameter Scan Time = 09:59:07; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513195; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; 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/2004-02/49665.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
1 592 632 148 218 444 414 612 622 155 220 464 404 0 0 156 230 63 55 100 94 98 90 858 868 1.072 .932 .871 .792 .962 1.946 52 301 .953 .63 80 1800 6170 93 101 68 76 0 675 233 442 .996 665 432 1.004 .93 -.005 -.104
2 882 808 149 222 733 586 884 819 155 224 735 597 0 0 148 151 38 52 100 100 100 100 1319 1332 1.251 .799 .812 .789 .773 1.246 32 219 .787 .849 70 1940 6160 92 99 82 89 0 863 237 626 .854 875 638 1.171 .868 -.227 -.204
3 1224 1256 149 216 1075 1040 1263 1346 155 219 1114 1130 0 0 284 289 39 53 100 100 100 98 2115 2244 1.034 .967 1.014 .945 .933 1.4 52 278 .972 .925 80 2090 6170 93 101 97 105 0 1342 231 1111 1.034 1438 1208 .967 1.084 .048 .116
4 731 607 153 224 578 383 710 645 157 227 557 421 0 0 137 134 38 56 100 96 100 96 961 978 1.509 .663 .756 .598 .641 1.903 32 212 .659 .723 70 2230 6160 92 99 111 118 0 649 239 409 .708 689 450 1.412 .808 -.498 -.308
5 1264 1246 150 210 1114 1036 1272 1260 156 212 1122 1050 0 0 281 278 38 54 100 100 100 100 2150 2172 1.075 .93 .936 .924 .93 1.233 52 336 .907 .923 90 2370 6160 91 100 124 133 0 1332 224 1107 .994 1346 1122 1.006 1 -.009 0
6 591 589 155 215 436 374 572 596 160 218 417 381 0 0 90 107 38 58 100 100 100 100 810 798 1.166 .858 .914 .84 .864 1.336 32 215 .866 .756 70 2510 6170 93 100 139 146 0 629 230 400 .917 637 407 1.091 .976 -.126 -.035
7 903 982 151 214 752 768 928 995 156 218 777 781 0 0 194 182 37 55 100 100 100 100 1520 1558 .979 1.021 1.005 1.026 1.026 1.226 52 338 1.005 .901 90 2660 6160 91 100 153 162 0 1049 229 821 1.091 1063 835 .916 1.074 .126 .103
8 1022 1106 148 205 874 901 1039 1084 153 209 891 879 0 0 156 256 36 54 100 100 100 100 1775 1770 .97 1.031 .987 1.003 .994 1.29 52 301 1.057 .906 90 2810 6160 91 100 168 177 0 1182 219 963 1.102 1158 939 .908 1.054 .14 .076
9 684 855 151 209 533 646 674 839 152 213 523 630 0 0 135 191 34 57 100 100 100 100 1179 1153 .825 1.212 1.205 1.187 1.264 1.362 52 257 1.223 .864 80 2950 6160 92 100 183 191 0 914 223 690 1.295 897 673 .772 1.287 .373 .364
10 1181 888 156 218 1025 670 1059 804 160 222 903 586 0 0 390 289 41 58 100 100 100 100 1695 1489 1.53 .654 .649 .638 .634 1.327 52 322 .629 .851 90 3100 6160 91 100 197 206 0 949 233 716 .699 859 626 1.432 .693 -.518 -.528
11 682 754 156 221 526 533 695 793 160 226 539 572 0 0 122 185 39 61 100 100 100 98 1059 1111 .987 1.013 1.061 .971 1.044 1.488 52 276 1.08 .814 80 3250 6160 92 100 213 221 0 806 236 570 1.083 847 611 .923 1.134 .115 .181
12 820 884 155 210 665 674 874 880 160 216 719 670 0 0 170 227 40 55 100 100 100 98 1339 1389 .987 1.014 .932 .983 .98 1.426 52 274 1.052 .849 80 3400 6160 92 100 228 236 0 945 224 720 1.083 940 716 .923 .996 .115 -.006
13 920 1102 154 218 766 884 923 1115 158 223 769 897 0 0 159 156 38 52 100 100 100 100 1650 1666 .867 1.154 1.166 1.163 1.155 1.229 52 306 1.146 .894 90 3540 6160 91 100 241 250 0 1178 233 945 1.233 1192 959 .811 1.246 .302 .318
14 1084 1368 156 215 928 1153 1108 1382 159 217 952 1167 0 0 157 185 39 52 100 100 100 100 2081 2119 .805 1.242 1.226 1.246 1.272 1.227 52 328 1.22 .909 90 3690 6160 91 100 256 265 0 1462 230 1232 1.328 1477 1247 .753 1.31 .409 .39
15 668 737 150 209 518 528 662 732 153 214 512 523 0 0 90 130 37 52 100 100 100 100 1046 1035 .981 1.019 1.021 1 1.015 1.333 52 264 1.033 .819 80 3840 6160 92 100 272 280 0 788 223 564 1.089 782 559 .918 1.092 .123 .126
16 1869 2118 149 212 1720 1906 1893 2173 151 215 1744 1961 0 0 420 470 36 49 100 100 100 100 3626 3705 .902 1.108 1.124 1.106 1.13 1.204 52 328 1.105 .943 90 3990 6160 91 100 286 295 0 2263 227 2037 1.184 2322 2096 .844 1.202 .244 .265
17 907 1062 149 208 758 854 925 1101 154 210 776 893 0 0 221 291 39 51 100 100 100 100 1612 1669 .888 1.127 1.151 1.09 1.146 1.434 52 254 1.154 .875 80 4140 6160 92 100 302 310 0 1135 222 913 1.204 1177 954 .831 1.23 .268 .298
18 1149 1357 157 203 992 1154 1196 1396 158 208 1039 1193 0 0 231 272 38 56 100 100 100 100 2146 2232 .86 1.163 1.148 1.168 1.14 1.231 52 302 1.136 .92 90 4280 6150 90 99 315 324 0 1450 217 1233 1.243 1492 1275 .804 1.227 .314 .295
19 2318 2491 150 203 2168 2288 2369 2626 154 208 2219 2423 0 0 802 962 44 57 100 100 100 98 4456 4642 .948 1.055 1.092 1.023 1.083 1.465 80 380 1.084 .935 100 4430 6160 91 101 330 340 0 2662 217 2445 1.128 2806 2589 .887 1.167 .173 .223
20 887 813 145 203 742 610 901 837 149 206 756 634 0 0 249 267 35 53 100 100 100 95 1352 1390 1.216 .822 .839 .768 .838 1.522 80 371 .856 .861 100 4580 6160 91 101 345 355 0 869 217 652 .879 894 678 1.138 .896 -.187 -.158

Total number of rows: 41664

Table truncated, full table size 9404 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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