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Sample GSM148711 Query DataSets for GSM148711
Status Public on Oct 03, 2007
Title PT05_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 52825.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT05_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT05_1 DNA
Prostate genomic DNA; LabeledExtract: 52825.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 = 1320, 6000; 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 = 38.72; Parameter Scan Time = 10:19:39; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166585; 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 = 38.72; Parameter Scan Time = 10:19:39; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531488; 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/2004-06/52825.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 GPL4639
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
1 494 409 197 220 297 189 505 406 205 223 308 186 0 0 103 105 79 69 98 92 92 69 486 494 1.571 .636 .604 .579 .628 2.01 52 286 .684 .482 80 1910 6670 63 71 55 63 0 442 238 204 .688 439 201 1.453 .653 -.539 -.615
2 834 796 195 234 639 562 828 778 198 241 633 544 0 0 195 208 45 72 100 100 98 96 1201 1177 1.137 .879 .859 .864 .93 1.421 52 264 .88 .806 80 2050 6670 63 71 69 77 0 861 253 608 .951 841 588 1.052 .929 -.073 -.106
3 583 569 198 230 385 339 590 563 203 236 392 333 0 0 77 109 48 70 100 100 100 96 724 725 1.136 .881 .849 .846 .857 1.472 32 220 .946 .586 70 2200 6670 63 70 84 91 0 615 249 367 .952 609 360 1.05 .918 -.071 -.123
4 523 520 192 225 331 295 514 494 200 228 322 269 0 0 87 100 49 64 100 100 100 93 626 591 1.122 .891 .835 .867 .89 1.547 32 227 .978 .634 70 2340 6660 62 69 98 105 0 562 243 319 .964 534 291 1.038 .903 -.054 -.147
5 522 548 188 238 334 310 501 539 190 240 313 301 0 0 96 114 43 67 100 100 100 98 644 614 1.077 .928 .962 .9 .936 1.527 52 277 1.007 .658 80 2490 6670 63 71 113 121 0 592 257 335 1.003 583 325 .997 1.04 .005 .056
6 466 438 194 233 272 205 464 454 195 237 270 221 0 0 70 102 44 66 100 87 100 68 477 491 1.327 .754 .819 .707 .763 1.925 32 164 .895 .429 60 2630 6670 64 70 128 134 0 474 252 222 .815 491 239 1.227 .885 -.295 -.176
7 498 503 186 223 312 280 511 491 189 227 325 268 0 0 107 101 42 64 100 100 96 90 592 593 1.114 .897 .825 .908 .914 1.867 32 228 .927 .547 70 2770 6670 63 70 141 148 0 544 241 303 .97 531 290 1.031 .892 -.044 -.166
8 767 754 198 248 569 506 778 722 203 255 580 474 0 0 179 192 49 77 100 100 100 96 1075 1054 1.125 .889 .817 .871 .844 1.494 32 218 .904 .74 70 2920 6660 62 69 156 163 0 815 268 547 .961 781 512 1.04 .884 -.057 -.179
9 733 891 200 258 533 633 734 937 201 262 534 679 0 0 103 185 43 72 100 100 100 98 1166 1213 .842 1.188 1.272 1.132 1.257 1.591 52 324 1.277 .772 90 3070 6660 61 70 170 179 0 963 279 684 1.284 1013 734 .779 1.375 .361 .459
10 1101 1255 193 259 908 996 1094 1255 197 267 901 996 0 0 122 214 40 73 100 100 100 100 1904 1897 .912 1.097 1.105 1.081 1.074 1.25 52 289 1.115 .868 90 3220 6670 62 71 185 194 0 1357 280 1077 1.186 1357 1077 .843 1.195 .246 .257
11 714 686 190 251 524 435 731 692 193 261 541 441 0 0 101 126 38 71 100 100 100 100 959 982 1.205 .83 .815 .81 .815 1.417 52 301 .831 .712 90 3360 6660 61 70 199 208 0 742 271 470 .898 748 477 1.114 .881 -.156 -.182
12 807 967 189 250 618 717 810 999 191 254 621 749 0 0 99 174 38 68 100 100 100 100 1335 1370 .862 1.16 1.206 1.138 1.186 1.355 52 317 1.186 .821 90 3510 6670 62 71 214 223 0 1045 270 775 1.254 1080 810 .797 1.304 .327 .383
13 863 953 193 249 670 704 862 929 196 256 669 680 0 0 171 170 40 69 100 100 100 100 1374 1349 .952 1.051 1.016 1.061 1.066 1.365 52 313 1.054 .817 90 3650 6660 61 70 228 237 0 1030 269 761 1.136 1004 735 .88 1.099 .184 .136
14 999 1064 194 268 805 796 973 1056 200 271 779 788 0 0 167 197 40 72 100 100 100 100 1601 1567 1.011 .989 1.012 .979 .965 1.279 52 327 .973 .838 90 3800 6660 61 70 243 252 0 1150 290 861 1.069 1142 852 .935 1.094 .096 .129
15 594 658 192 234 402 424 589 668 196 240 397 434 0 0 111 153 40 69 100 98 98 97 826 831 .948 1.055 1.093 1.018 1.03 1.556 80 325 1.116 .715 100 3950 6670 62 72 258 268 0 711 253 458 1.14 722 469 .877 1.182 .189 .241
16 1395 1815 183 229 1212 1586 1483 1897 185 237 1300 1668 0 0 515 609 40 72 100 100 97 100 2798 2968 .764 1.309 1.283 1.386 1.349 1.515 80 328 1.288 .895 100 4090 6670 62 72 272 282 0 1962 248 1715 1.415 2051 1803 .707 1.387 .501 .472
17 792 790 179 236 613 554 807 824 183 244 628 588 0 0 120 137 41 69 100 100 100 100 1167 1216 1.106 .904 .936 .89 .95 1.32 52 289 .947 .821 90 4240 6660 61 70 287 296 0 854 255 599 .977 891 636 1.023 1.012 -.033 .018
18 1007 975 177 239 830 736 1016 975 182 245 839 736 0 0 185 177 39 65 100 100 100 100 1566 1575 1.128 .887 .877 .881 .849 1.46 52 290 .901 .808 90 4380 6660 61 70 301 310 0 1054 258 796 .959 1054 796 1.043 .948 -.061 -.076
19 1702 1867 185 252 1517 1615 1801 1889 190 253 1616 1637 0 0 521 519 51 69 100 100 98 100 3132 3253 .939 1.065 1.013 1.111 1.028 1.445 80 341 1.059 .929 100 4530 6670 62 72 316 326 0 2019 272 1746 1.151 2042 1770 .869 1.095 .203 .131
20 908 838 195 244 713 594 902 826 199 251 707 582 0 0 137 138 56 73 100 100 100 100 1307 1289 1.2 .833 .823 .827 .829 1.316 52 300 .813 .807 90 4670 6660 61 70 330 339 0 906 264 642 .901 893 629 1.11 .89 -.151 -.168

Total number of rows: 41472

Table truncated, full table size 9324 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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