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Sample GSM148707 Query DataSets for GSM148707
Status Public on Oct 03, 2007
Title PT168_2 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49676.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT168_2 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT168_2 DNA
Prostate genomic DNA; LabeledExtract: 49676.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 = 37.96; Parameter Scan Time = 09:02:28; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149933; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; 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 = 37.96; Parameter Scan Time = 09:02:28; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514836; 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/2004-02/49676.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
1 848 1042 182 259 666 783 819 1055 185 264 637 796 0 0 196 245 43 59 100 100 100 100 1449 1433 .851 1.176 1.25 1.17 1.17 1.241 52 354 1.172 .888 90 1600 5950 82 91 71 80 0 928 231 697 1.047 939 709 .955 1.113 .066 .154
2 1276 1168 180 256 1096 912 1330 1220 184 263 1150 964 0 0 299 370 40 59 100 100 100 96 2008 2114 1.202 .832 .838 .762 .798 1.611 32 231 .829 .868 70 1750 5940 82 89 87 94 0 1040 228 812 .741 1086 858 1.35 .746 -.432 -.422
3 1814 2308 179 248 1635 2060 1988 2491 182 253 1809 2243 0 0 502 662 41 53 100 100 100 100 3695 4052 .794 1.26 1.24 1.263 1.309 1.181 52 352 1.26 .96 90 1910 5950 82 91 102 111 0 2055 221 1834 1.122 2218 1997 .891 1.104 .166 .143
4 1234 917 178 250 1056 667 1264 880 182 253 1086 630 0 0 238 242 37 51 100 100 100 100 1723 1716 1.583 .632 .58 .607 .602 1.329 32 219 .632 .866 70 2060 5940 82 89 118 125 0 817 223 594 .562 784 561 1.778 .517 -.83 -.953
5 1977 2012 177 250 1800 1762 2030 2053 183 255 1853 1803 0 0 453 519 44 60 100 100 100 100 3562 3656 1.022 .979 .973 .956 .971 1.264 52 332 .985 .951 90 2200 5940 81 90 131 140 0 1792 223 1569 .872 1828 1606 1.147 .866 -.198 -.207
6 794 659 173 246 621 413 813 665 178 255 640 419 0 0 189 216 43 62 100 93 100 87 1034 1059 1.504 .665 .655 .589 .644 1.631 32 161 .641 .686 60 2340 5950 84 90 147 153 0 587 219 368 .592 592 373 1.689 .583 -.756 -.778
7 1532 1794 166 239 1366 1555 1607 1782 168 246 1441 1543 0 0 342 418 36 54 100 100 100 100 2921 2984 .878 1.138 1.071 1.138 1.101 1.244 52 275 1.152 .936 80 2480 5950 83 91 160 168 0 1598 213 1385 1.014 1587 1374 .987 .954 .02 -.069
8 1301 1668 166 231 1135 1437 1322 1781 168 233 1156 1550 0 0 412 512 35 54 100 100 100 100 2572 2706 .79 1.266 1.341 1.254 1.301 1.326 52 254 1.271 .935 80 2640 5940 82 90 176 184 0 1485 206 1280 1.127 1586 1380 .887 1.194 .173 .256
9 822 1103 169 223 653 880 864 1113 173 227 695 890 0 0 269 372 58 54 100 100 94 100 1533 1585 .742 1.348 1.281 1.39 1.389 1.456 52 307 1.354 .899 90 2770 5940 81 90 188 197 0 982 199 784 1.2 991 793 .833 1.14 .263 .189
10 1374 1490 171 230 1203 1260 1384 1478 175 232 1213 1248 0 0 269 361 41 55 100 100 100 100 2463 2461 .955 1.047 1.029 1.023 1.049 1.257 52 320 1.072 .933 90 2940 5940 81 90 205 214 0 1327 205 1122 .933 1316 1111 1.072 .916 -.101 -.126
11 698 755 169 234 529 521 715 729 169 236 546 495 0 0 153 189 36 55 100 98 100 98 1050 1041 1.015 .985 .907 .948 1.017 1.53 52 266 1.047 .857 80 3080 5940 82 90 220 228 0 672 208 464 .877 649 441 1.14 .807 -.189 -.309
12 681 826 170 231 511 595 688 832 175 234 518 601 0 0 183 243 40 55 100 98 98 98 1106 1119 .859 1.164 1.16 1.138 1.197 1.403 52 267 1.17 .837 80 3230 5940 82 90 235 243 0 736 206 530 1.037 741 535 .964 1.033 .052 .047
13 858 1095 169 230 689 865 820 1078 173 233 651 848 0 0 268 326 40 54 100 100 100 100 1554 1499 .797 1.255 1.303 1.244 1.276 1.379 52 288 1.269 .894 90 3370 5940 81 90 248 257 0 975 205 770 1.118 960 755 .895 1.16 .161 .214
14 859 1141 169 226 690 915 942 1224 173 232 773 998 0 0 305 408 51 54 97 98 93 96 1605 1771 .754 1.326 1.291 1.365 1.281 1.578 80 395 1.339 .933 100 3510 5940 81 91 262 272 0 1016 201 815 1.181 1090 889 .847 1.15 .24 .201
15 713 783 170 227 543 556 694 815 177 230 524 588 0 0 221 170 56 52 100 100 100 98 1099 1112 .977 1.024 1.122 1.03 1.122 1.426 52 324 .98 .76 90 3670 5940 81 90 278 287 0 697 202 495 .912 726 524 1.097 .999 -.133 -.001
16 1922 2740 172 221 1750 2519 2070 2837 179 226 1898 2616 0 0 560 812 46 53 100 100 100 100 4269 4514 .695 1.439 1.378 1.423 1.458 1.326 52 279 1.446 .953 80 3820 5940 82 90 294 302 0 2440 197 2243 1.282 2526 2329 .78 1.227 .358 .296
17 905 1190 170 228 735 962 890 1221 180 236 720 993 0 0 243 316 63 61 100 100 100 100 1697 1713 .764 1.309 1.379 1.286 1.297 1.37 32 200 1.319 .855 70 3950 5930 81 88 307 314 0 1060 203 857 1.165 1087 884 .858 1.228 .221 .296
18 1147 916 175 221 972 695 1202 965 178 231 1027 744 0 0 241 253 44 58 100 98 100 98 1667 1771 1.399 .715 .724 .702 .721 1.371 52 313 .735 .893 90 4100 5940 81 90 321 330 0 816 197 619 .637 859 663 1.571 .645 -.651 -.632
19 2054 2436 175 225 1879 2211 2098 2429 181 231 1923 2204 0 0 906 1115 62 62 97 100 96 98 4090 4127 .85 1.177 1.146 1.284 1.185 1.9 80 355 1.191 .95 100 4240 5940 81 91 335 345 0 2169 200 1969 1.048 2163 1963 .954 1.021 .067 .029
20 937 951 169 227 768 724 997 1015 176 231 828 788 0 0 315 307 62 57 98 98 95 97 1492 1616 1.061 .943 .952 .951 .96 1.587 80 391 .932 .9 100 4380 5940 81 91 349 359 0 847 202 645 .839 904 702 1.191 .847 -.252 -.239

Total number of rows: 41664

Table truncated, full table size 9635 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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