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Sample GSM148700 Query DataSets for GSM148700
Status Public on Oct 03, 2007
Title PT317_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 48002.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT317_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT317_2 DNA
Prostate genomic DNA; LabeledExtract: 48002.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 = 800, 4960; 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 = 38.66; Parameter Scan Time = 11:52:27; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142656; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; 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 = 38.66; Parameter Scan Time = 11:52:27; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; 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/2004-01/48002.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
1 810 710 149 174 661 536 843 733 230 179 694 559 0 0 192 159 933 66 3 100 0 100 1197 1253 1.233 .811 .805 .822 .823 1.411 32 216 .773 .823 70 1750 6120 112 119 91 98 0 671 164 507 .766 693 528 1.305 .761 -.384 -.394
2 1284 847 150 170 1134 677 1389 837 150 171 1239 667 0 0 408 213 33 39 100 100 100 100 1811 1906 1.675 .597 .538 .643 .591 1.596 32 226 .54 .848 70 1910 6120 112 119 107 114 0 800 161 640 .564 791 630 1.772 .509 -.826 -.975
3 1400 1473 148 170 1252 1303 1545 1585 150 172 1397 1415 0 0 465 467 35 41 100 100 100 100 2555 2812 .961 1.041 1.013 1.053 1.018 1.425 52 284 1.031 .926 80 2060 6120 112 120 122 130 0 1392 161 1231 .984 1498 1337 1.017 .957 -.024 -.063
4 1283 729 144 164 1139 565 1307 716 149 168 1163 552 0 0 269 165 33 37 100 100 100 100 1704 1715 2.016 .496 .475 .489 .515 1.349 32 170 .475 .853 60 2210 6120 113 119 138 144 0 689 155 534 .469 677 522 2.133 .449 -1.093 -1.157
5 1561 1390 148 167 1413 1223 1645 1408 151 171 1497 1241 0 0 399 312 53 47 100 100 100 100 2636 2738 1.155 .866 .829 .882 .858 1.348 52 282 .847 .913 80 2350 6120 112 120 151 159 0 1314 158 1156 .818 1331 1173 1.222 .783 -.29 -.352
6 996 590 143 175 853 415 1064 626 151 179 921 451 0 0 299 203 60 48 100 96 100 90 1268 1372 2.055 .487 .49 .42 .473 1.796 32 212 .479 .828 70 2490 6110 111 118 165 172 0 558 165 392 .46 592 426 2.175 .463 -1.121 -1.112
7 1192 1177 145 165 1047 1012 1242 1288 149 169 1097 1123 0 0 310 331 33 42 100 100 100 100 2059 2220 1.035 .967 1.024 .938 .959 1.345 52 278 .979 .923 80 2650 6120 112 120 181 189 0 1112 156 956 .913 1217 1061 1.095 .967 -.131 -.048
8 1228 1197 148 163 1080 1034 1348 1235 151 166 1200 1072 0 0 299 291 38 43 100 100 100 100 2114 2272 1.044 .957 .893 .964 .942 1.328 32 201 .93 .903 70 2780 6110 111 118 194 201 0 1131 154 977 .905 1167 1013 1.105 .844 -.144 -.244
9 1138 815 155 170 983 645 1165 807 184 186 1010 637 0 0 232 182 147 90 100 100 100 100 1628 1647 1.524 .656 .631 .651 .638 1.358 32 226 .447 .945 70 2920 6100 110 117 208 215 0 770 161 610 .62 763 602 1.613 .596 -.689 -.746
10 1441 1293 149 162 1292 1131 1478 1350 154 167 1329 1188 0 0 323 260 46 49 100 100 100 100 2423 2517 1.142 .875 .894 .886 .864 1.248 52 323 .855 .931 90 3080 6120 111 120 223 232 0 1222 153 1069 .827 1276 1123 1.209 .845 -.273 -.243
11 741 744 150 169 591 575 750 770 155 176 600 601 0 0 258 202 37 45 100 100 100 100 1166 1201 1.028 .973 1.002 1.017 1.038 1.505 52 279 .928 .847 80 3230 6120 112 120 239 247 0 703 160 543 .919 728 568 1.088 .947 -.121 -.079
12 1107 1072 155 179 952 893 1120 1096 156 184 965 917 0 0 273 177 37 49 100 100 100 100 1845 1882 1.066 .938 .95 .99 .953 1.428 32 218 .895 .905 70 3370 6110 111 118 253 260 0 1013 169 844 .887 1036 867 1.128 .898 -.174 -.155
13 1099 1233 147 166 952 1067 1138 1289 149 169 991 1123 0 0 343 431 33 45 98 98 98 98 2019 2114 .892 1.121 1.133 1.114 1.118 1.973 52 274 1.161 .916 80 3520 6110 111 119 268 276 0 1165 157 1008 1.059 1218 1061 .944 1.071 .083 .099
14 1412 1555 149 177 1263 1378 1472 1679 151 181 1323 1502 0 0 292 365 34 48 100 100 100 100 2641 2825 .917 1.091 1.135 1.071 1.084 1.298 52 338 1.103 .939 90 3670 6110 110 119 282 291 0 1470 167 1302 1.031 1587 1420 .97 1.073 .044 .102
15 811 861 147 173 664 688 834 899 150 177 687 726 0 0 172 218 36 44 100 100 98 100 1352 1413 .965 1.036 1.057 1.014 1.027 1.451 52 269 1.061 .901 80 3820 6110 111 119 298 306 0 814 163 650 .979 850 686 1.021 .999 -.03 -.002
16 2649 3209 142 163 2507 3046 2758 3312 147 169 2616 3149 0 0 1319 1622 45 49 100 100 100 100 5553 5765 .823 1.215 1.204 1.166 1.21 1.558 52 271 1.224 .959 80 3970 6110 111 119 313 321 0 3033 154 2879 1.148 3130 2976 .871 1.138 .199 .186
17 1232 1303 148 181 1084 1122 1256 1300 154 184 1108 1119 0 0 281 322 49 53 100 100 100 100 2206 2227 .966 1.035 1.01 1.028 1.079 1.332 32 209 1.048 .917 70 4100 6110 111 118 326 333 0 1231 171 1060 .978 1229 1058 1.022 .954 -.032 -.067
18 1231 1357 151 173 1080 1184 1308 1428 163 187 1157 1255 0 0 374 362 82 86 100 100 100 100 2264 2412 .912 1.096 1.085 1.117 1.079 1.311 32 223 1.046 .929 70 4240 6100 110 117 340 347 0 1282 163 1119 1.036 1350 1186 .965 1.025 .051 .036
19 2928 3072 148 170 2780 2902 2732 2659 151 173 2584 2489 0 0 1104 1138 45 50 100 100 100 100 5682 5073 .958 1.044 .963 1.057 1.053 1.314 52 278 1.037 .96 80 4390 6110 111 119 355 363 0 2903 161 2743 .987 2513 2352 1.014 .91 -.02 -.136
20 998 913 142 163 856 750 1002 949 147 169 860 786 0 0 298 245 32 42 100 100 100 100 1606 1646 1.141 .876 .914 .901 .895 1.382 52 275 .864 .913 80 4530 6110 111 119 369 377 0 863 154 709 .828 897 743 1.208 .864 -.272 -.211

Total number of rows: 41664

Table truncated, full table size 9678 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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