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Sample GSM148709 Query DataSets for GSM148709
Status Public on Oct 03, 2007
Title PT111_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49678.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT111_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT111_1 DNA
Prostate genomic DNA; LabeledExtract: 49678.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 = 38.21; Parameter Scan Time = 09:18:41; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149950; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; 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 = 38.21; Parameter Scan Time = 09:18:41; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514853; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; 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/2004-02/49678.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
1 786 813 160 209 626 604 789 840 163 213 629 631 0 0 136 170 37 51 100 100 100 100 1230 1260 1.036 .965 1.003 .943 .975 1.335 32 197 .934 .826 70 1640 5960 84 91 76 83 0 729 187 542 .866 754 566 1.155 .9 -.208 -.152
2 1061 586 156 211 905 375 1085 613 170 220 929 402 0 0 272 172 96 79 100 90 100 90 1280 1331 2.413 .414 .433 .359 .391 1.859 32 171 .434 .676 60 1800 5950 84 90 93 99 0 526 189 336 .372 550 361 2.69 .388 -1.428 -1.365
3 1249 1230 163 221 1086 1009 1320 1266 172 225 1157 1045 0 0 309 356 56 55 100 100 98 100 2095 2202 1.076 .929 .903 .915 .951 1.301 52 277 .947 .899 80 1940 5960 84 92 106 114 0 1103 198 905 .834 1136 937 1.2 .81 -.263 -.304
4 1077 488 165 227 912 261 1093 490 180 240 928 263 0 0 496 160 112 96 92 84 88 67 1173 1191 3.494 .286 .283 .308 .343 2.627 52 243 .266 .48 80 2090 5970 85 93 121 129 0 438 204 234 .257 440 236 3.895 .254 -1.962 -1.976
5 1348 1192 154 215 1194 977 1365 1169 159 214 1211 954 0 0 388 366 44 51 100 100 100 100 2171 2165 1.222 .818 .788 .803 .78 1.426 52 333 .822 .917 90 2230 5960 83 92 134 143 0 1069 193 876 .734 1049 856 1.362 .707 -.446 -.501
6 827 443 154 210 673 233 848 446 159 209 694 236 0 0 151 121 40 52 100 96 100 81 906 930 2.888 .346 .34 .301 .33 1.749 32 172 .325 .548 60 2390 5960 85 91 152 158 0 397 188 209 .311 400 212 3.22 .305 -1.687 -1.713
7 1147 1233 157 213 990 1020 1184 1267 163 215 1027 1054 0 0 204 256 47 58 100 100 100 100 2010 2081 .971 1.03 1.026 1.02 1.025 1.235 32 223 1.053 .923 70 2520 5950 83 90 164 171 0 1106 191 915 .924 1137 946 1.082 .921 -.114 -.119
8 1096 1251 154 208 942 1043 1110 1250 157 213 956 1042 0 0 121 205 40 55 100 100 100 100 1985 1998 .903 1.107 1.09 1.094 1.129 1.195 32 233 1.107 .911 70 2670 5950 83 90 179 186 0 1122 187 936 .993 1121 935 1.007 .978 -.01 -.032
9 776 942 155 202 621 740 797 954 157 207 642 752 0 0 181 218 37 52 100 100 100 100 1361 1394 .839 1.192 1.171 1.195 1.2 1.249 32 226 1.203 .917 70 2820 5950 83 90 194 201 0 845 181 664 1.069 856 675 .935 1.051 .096 .072
10 1076 1008 151 221 925 787 1161 1023 154 223 1010 802 0 0 306 295 38 52 98 100 98 100 1712 1812 1.175 .851 .794 .857 .829 1.526 52 283 .861 .927 80 2970 5960 84 92 209 217 0 904 198 706 .763 918 719 1.31 .712 -.39 -.489
11 753 884 153 200 600 684 728 893 156 205 575 693 0 0 127 148 38 51 100 100 100 100 1284 1268 .877 1.14 1.205 1.137 1.104 1.229 32 222 1.162 .886 70 3130 5950 83 90 225 232 0 793 179 614 1.023 801 622 .978 1.081 .032 .113
12 832 851 160 207 672 644 908 871 168 217 748 664 0 0 218 193 58 70 100 100 100 100 1316 1412 1.043 .958 .888 .972 .975 1.289 32 220 .956 .871 70 3260 5940 82 89 238 245 0 763 186 578 .86 781 596 1.163 .796 -.218 -.328
13 863 1169 160 205 703 964 890 1242 163 208 730 1037 0 0 291 335 43 50 100 100 96 98 1667 1767 .729 1.371 1.421 1.426 1.451 1.371 52 252 1.343 .926 80 3440 5950 83 91 256 264 0 1049 184 865 1.23 1114 930 .813 1.274 .299 .35
14 968 1232 159 200 809 1032 1019 1274 167 205 860 1074 0 0 203 280 71 50 100 100 100 100 1841 1934 .784 1.276 1.249 1.263 1.294 1.301 52 256 1.284 .929 80 3550 5950 83 91 267 275 0 1105 179 926 1.144 1143 964 .874 1.12 .195 .164
15 736 864 162 204 574 660 766 887 170 218 604 683 0 0 136 153 60 72 100 100 100 100 1234 1287 .87 1.15 1.131 1.165 1.097 1.423 32 220 1.185 .857 70 3700 5940 82 89 282 289 0 775 183 592 1.032 796 613 .969 1.014 .045 .021
16 1804 2265 154 206 1650 2059 1966 2381 155 201 1812 2175 0 0 715 847 38 49 100 100 100 100 3709 3987 .801 1.248 1.2 1.262 1.239 1.266 52 301 1.239 .962 80 3870 5950 83 91 299 307 0 2032 185 1847 1.119 2136 1951 .893 1.077 .163 .107
17 961 1236 155 212 806 1024 973 1211 158 209 818 999 0 0 185 243 38 58 100 100 100 100 1830 1817 .787 1.27 1.221 1.271 1.258 1.22 32 217 1.29 .93 70 4020 5950 83 90 314 321 0 1109 190 919 1.14 1086 896 .877 1.096 .189 .132
18 1164 1281 150 219 1014 1062 1191 1285 153 220 1041 1066 0 0 189 211 37 51 100 100 100 100 2076 2107 .955 1.047 1.024 1.044 1.023 1.219 32 206 1.079 .921 70 4160 5950 83 90 328 335 0 1149 196 953 .94 1153 956 1.064 .919 -.09 -.122
19 2181 2339 150 213 2031 2126 2247 2425 156 212 2097 2212 0 0 651 691 37 49 100 100 100 100 4157 4309 .955 1.047 1.055 1.056 1.043 1.264 52 242 1.05 .965 80 4290 5960 84 92 341 349 0 2098 191 1907 .939 2176 1984 1.065 .946 -.091 -.08
20 943 818 148 203 795 615 1007 829 153 210 859 626 0 0 260 225 39 55 100 100 100 100 1410 1485 1.293 .774 .729 .77 .789 1.311 52 275 .786 .902 80 4430 5960 84 92 355 363 0 734 182 552 .694 744 562 1.441 .654 -.527 -.613

Total number of rows: 41664

Table truncated, full table size 9576 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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