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Sample GSM148752 Query DataSets for GSM148752
Status Public on Oct 03, 2007
Title PT96_1 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49666.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PT96_1 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PT96_1 DNA
Prostate genomic DNA; LabeledExtract: 49666.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 = 1080, 5200; 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 = 38.35; Parameter Scan Time = 10:12:44; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148305; 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 = 38.35; Parameter Scan Time = 10:12:44; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513208; 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/2004-02/49666.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
1 478 497 131 175 347 322 497 524 132 179 366 349 0 0 140 160 35 48 100 94 98 86 669 715 1.078 .928 .954 .85 .995 1.762 52 300 .977 .74 80 1820 5980 74 82 70 78 0 569 200 369 1.063 600 400 .941 1.092 .088 .127
2 740 615 133 178 607 437 763 634 134 177 630 456 0 0 130 135 32 48 100 100 100 100 1044 1086 1.389 .72 .724 .692 .721 1.443 32 164 .752 .82 60 1950 5970 74 80 84 90 0 704 204 501 .825 726 522 1.213 .829 -.278 -.271
3 969 938 136 172 833 766 1015 964 139 178 879 792 0 0 211 209 33 49 100 100 100 100 1599 1671 1.087 .92 .901 .914 .936 1.287 52 330 .904 .902 90 2100 5980 73 82 97 106 0 1074 197 877 1.053 1104 907 .949 1.032 .075 .045
4 644 392 140 175 504 217 637 400 142 180 497 225 0 0 131 83 30 51 100 100 100 93 721 722 2.323 .431 .453 .412 .417 1.438 32 165 .414 .688 60 2240 5970 74 80 113 119 0 449 200 249 .493 458 258 2.028 .519 -1.02 -.948
5 969 586 130 173 839 413 819 459 134 179 689 286 0 0 434 346 37 51 100 98 100 92 1252 975 2.031 .492 .415 .406 .429 1.656 52 355 .553 .822 90 2380 5970 72 81 125 134 0 671 198 473 .564 526 328 1.774 .475 -.827 -1.073
6 570 231 132 186 438 45 567 213 133 189 435 27 0 0 98 81 33 53 100 28 100 15 483 462 9.733 .103 .062 .112 .092 2.469 32 214 .092 .068 70 2530 5980 74 81 141 148 0 265 213 52 .118 244 31 8.498 .071 -3.087 -3.814
7 820 759 128 183 692 576 841 784 136 188 713 601 0 0 170 180 55 60 100 100 100 100 1268 1314 1.201 .832 .843 .811 .799 1.257 52 338 .888 .886 90 2680 5970 72 81 155 164 0 869 210 660 .953 898 688 1.049 .965 -.069 -.051
8 758 711 131 178 627 533 786 745 132 183 655 567 0 0 134 169 31 49 100 100 100 98 1160 1222 1.176 .85 .866 .81 .869 1.404 52 290 .902 .858 90 2820 5970 72 81 169 178 0 814 204 610 .974 853 649 1.027 .991 -.039 -.012
9 556 598 134 185 422 413 566 601 136 185 432 416 0 0 87 130 32 50 100 100 100 98 835 848 1.022 .979 .963 .94 .973 1.4 52 299 1.034 .822 90 2960 5970 72 81 183 192 0 685 212 473 1.121 688 476 .892 1.103 .165 .141
10 884 780 136 181 748 599 905 773 137 184 769 592 0 0 208 182 31 46 100 100 100 100 1347 1361 1.249 .801 .77 .786 .783 1.353 52 325 .787 .867 90 3110 5970 72 81 198 207 0 893 207 686 .917 885 678 1.09 .882 -.125 -.182
11 500 455 133 180 367 275 511 453 138 189 378 273 0 0 88 107 36 52 100 98 100 98 642 651 1.335 .749 .722 .688 .767 1.752 52 284 .814 .704 80 3260 5970 73 81 214 222 0 521 206 315 .858 519 313 1.165 .827 -.221 -.274
12 609 623 136 180 473 443 609 633 140 185 473 453 0 0 104 122 39 51 100 100 100 98 916 926 1.068 .937 .958 .919 .932 1.319 52 344 .973 .85 90 3410 5970 72 81 228 237 0 714 206 507 1.073 725 519 .932 1.097 .101 .133
13 713 755 134 172 579 583 684 761 136 179 550 589 0 0 90 131 35 50 100 100 100 100 1162 1139 .993 1.007 1.071 .989 1.03 1.293 52 312 1.048 .866 90 3560 5970 72 81 243 252 0 865 197 668 1.153 872 675 .867 1.227 .206 .295
14 791 789 138 175 653 614 787 789 141 184 649 614 0 0 105 152 35 51 100 100 100 100 1267 1263 1.064 .94 .946 .921 .922 1.348 52 325 .98 .859 90 3700 5970 72 81 257 266 0 904 200 703 1.077 904 703 .929 1.084 .107 .116
15 469 465 135 179 334 286 472 458 138 189 337 279 0 0 77 92 33 52 100 98 100 96 620 616 1.168 .856 .828 .821 .861 1.515 52 252 .894 .676 80 3850 5970 73 81 273 281 0 533 205 328 .981 525 320 1.02 .948 -.028 -.077
16 1557 1610 133 182 1424 1428 1591 1615 135 187 1458 1433 0 0 273 378 32 50 100 100 100 100 2852 2891 .997 1.003 .983 .98 1.03 1.247 52 328 1.041 .934 90 4000 5970 72 81 287 296 0 1844 208 1636 1.149 1850 1641 .871 1.126 .2 .171
17 773 810 139 186 634 624 776 806 141 187 637 620 0 0 165 191 34 50 100 100 100 100 1258 1257 1.016 .984 .973 .961 .987 1.388 52 254 .994 .874 80 4150 5970 73 81 303 311 0 928 213 715 1.127 923 710 .887 1.115 .173 .157
18 774 766 135 186 639 580 803 774 136 190 668 588 0 0 142 142 31 48 100 100 100 100 1219 1256 1.102 .908 .88 .909 .877 1.31 52 300 .926 .881 90 4290 5970 72 81 316 325 0 877 213 664 1.04 887 673 .962 1.008 .056 .012
19 1648 1689 132 181 1516 1508 1665 1703 134 184 1533 1522 0 0 716 769 34 46 98 98 97 95 3024 3055 1.005 .995 .993 .976 .968 1.511 80 388 1.014 .956 100 4440 5970 72 82 331 341 0 1935 207 1727 1.139 1951 1743 .878 1.137 .188 .185
20 631 541 138 179 493 362 660 527 139 180 522 348 0 0 122 118 34 47 100 100 100 100 855 870 1.362 .734 .667 .722 .719 1.4 52 312 .723 .78 90 4580 5970 72 81 345 354 0 620 205 415 .841 604 399 1.189 .764 -.25 -.389

Total number of rows: 41664

Table truncated, full table size 9413 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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