NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM148759 Query DataSets for GSM148759
Status Public on Oct 03, 2007
Title PT176_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 47166.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL176_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL176_2 DNA
Prostate genomic DNA; LabeledExtract: 47166.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 = 1120, 5530; 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 = 38.67; Parameter Scan Time = 11:14:38; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135314; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.49; 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 = 38.67; Parameter Scan Time = 11:14:38; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500379; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.00; 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/2003-12/47166.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
1 656 553 149 201 507 352 652 548 151 206 503 347 0 0 85 115 33 54 100 98 100 98 859 850 1.44 .694 .69 .65 .735 1.658 52 345 .691 .713 90 1860 6240 66 75 69 78 0 639 232 407 .802 633 401 1.247 .797 -.318 -.328
2 987 611 151 199 836 412 1029 621 154 204 878 422 0 0 256 153 35 56 100 98 100 98 1248 1300 2.029 .493 .481 .458 .506 1.873 52 248 .477 .818 80 2000 6250 68 76 84 92 0 706 230 476 .569 717 487 1.757 .555 -.813 -.849
3 1152 901 152 195 1000 706 1131 883 153 199 979 688 0 0 114 138 34 54 100 100 100 100 1706 1667 1.416 .706 .703 .698 .697 1.21 52 305 .722 .898 90 2140 6250 67 76 97 106 0 1041 225 816 .816 1020 795 1.226 .812 -.294 -.301
4 1094 313 151 197 943 116 1117 307 156 203 966 110 0 0 207 103 38 58 100 68 100 50 1059 1076 8.129 .123 .114 .108 .132 2.394 32 207 .124 .314 70 2280 6240 67 74 112 119 0 362 228 134 .142 355 127 7.037 .132 -2.815 -2.926
5 1162 936 151 194 1011 742 1196 929 153 200 1045 735 0 0 280 196 35 54 100 100 100 100 1753 1780 1.363 .734 .703 .745 .718 1.318 80 393 .717 .905 100 2430 6250 67 77 126 136 0 1081 224 857 .848 1073 849 1.18 .812 -.238 -.3
6 771 465 155 201 616 264 769 485 158 205 614 284 0 0 91 93 35 51 100 100 100 93 880 898 2.333 .429 .463 .402 .445 1.546 32 198 .439 .62 70 2570 6240 67 74 141 148 0 537 232 305 .495 560 328 2.02 .534 -1.014 -.904
7 1048 1016 155 198 893 818 1029 1016 157 201 874 818 0 0 162 179 37 49 100 100 100 100 1711 1692 1.092 .916 .936 .907 .918 1.229 52 313 .944 .917 90 2720 6240 66 75 155 164 0 1174 229 945 1.058 1174 945 .945 1.081 .082 .113
8 918 769 156 196 762 573 904 763 161 199 748 567 0 0 138 151 35 50 100 100 100 100 1335 1315 1.33 .752 .758 .736 .734 1.312 52 302 .756 .85 90 2860 6240 66 75 169 178 0 888 226 662 .869 881 655 1.151 .876 -.203 -.192
9 819 727 160 197 659 530 810 693 162 203 650 496 0 0 118 114 37 56 100 100 100 100 1189 1146 1.243 .804 .763 .801 .796 1.286 52 300 .801 .854 90 3010 6240 66 75 184 193 0 840 228 612 .929 801 573 1.076 .881 -.106 -.182
10 1327 904 158 196 1169 708 1300 910 161 200 1142 714 0 0 160 119 37 59 100 100 100 100 1877 1856 1.651 .606 .625 .602 .618 1.233 52 301 .594 .892 90 3160 6240 66 75 199 208 0 1044 226 818 .7 1051 825 1.429 .722 -.515 -.469
11 713 698 157 200 556 498 691 712 162 200 534 512 0 0 111 151 37 51 100 100 100 100 1054 1046 1.116 .896 .959 .866 .885 1.319 52 301 .921 .854 90 3300 6240 66 75 213 222 0 806 231 575 1.035 822 591 .967 1.108 .049 .147
12 972 790 156 197 816 593 972 780 161 199 816 583 0 0 146 129 39 52 100 100 100 100 1409 1399 1.376 .727 .714 .722 .718 1.291 52 313 .736 .862 90 3450 6240 66 75 228 237 0 913 228 685 .839 901 673 1.191 .825 -.252 -.277
13 1040 1065 155 198 885 867 1028 1035 160 201 873 837 0 0 107 126 37 56 100 100 100 100 1752 1710 1.021 .98 .959 .976 .947 1.217 52 300 .997 .904 90 3600 6240 66 75 243 252 0 1230 229 1002 1.132 1196 967 .884 1.108 .178 .147
14 1109 1218 158 201 951 1017 1153 1284 159 201 995 1083 0 0 204 243 35 54 100 100 100 100 1968 2078 .935 1.069 1.088 1.06 1.063 1.27 80 358 1.082 .926 100 3750 6240 66 76 258 268 0 1407 232 1175 1.235 1483 1251 .81 1.257 .305 .33
15 709 803 154 207 555 596 711 829 156 210 557 622 0 0 100 107 35 57 100 100 100 100 1151 1179 .931 1.074 1.117 1.072 1.105 1.29 52 288 1.096 .859 90 3890 6240 66 75 272 281 0 928 239 688 1.24 958 719 .806 1.29 .311 .367
16 1949 1472 149 198 1800 1274 1921 1518 153 203 1772 1320 0 0 452 282 35 59 100 100 100 100 3074 3092 1.413 .708 .745 .711 .71 1.171 52 316 .696 .945 90 4040 6240 66 75 287 296 0 1700 229 1472 .818 1754 1525 1.223 .86 -.291 -.217
17 1266 1203 153 198 1113 1005 1271 1231 156 202 1118 1033 0 0 222 218 41 57 100 100 100 100 2118 2151 1.107 .903 .924 .896 .88 1.228 52 242 .91 .924 80 4180 6240 67 75 302 310 0 1390 229 1161 1.043 1422 1193 .959 1.067 .061 .094
18 1210 1043 149 209 1061 834 1293 1113 152 207 1144 904 0 0 290 266 35 50 100 100 100 100 1895 2048 1.272 .786 .79 .767 .78 1.22 80 330 .793 .943 100 4340 6240 66 76 317 327 0 1205 241 963 .908 1286 1044 1.101 .913 -.139 -.132
19 3143 3130 147 198 2996 2932 3206 3126 148 200 3059 2928 0 0 881 761 33 53 100 100 100 100 5928 5987 1.022 .979 .957 1.002 .976 1.207 80 319 .957 .964 100 4480 6240 66 76 331 341 0 3616 229 3387 1.13 3611 3382 .885 1.106 .177 .145
20 1122 738 153 192 969 546 1152 760 152 198 999 568 0 0 176 142 33 52 100 100 100 100 1515 1567 1.775 .563 .569 .552 .558 1.31 80 349 .559 .868 100 4630 6240 66 76 346 356 0 852 222 631 .651 878 656 1.536 .657 -.62 -.607

Total number of rows: 41664

Table truncated, full table size 9560 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap