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Sample GSM148754 Query DataSets for GSM148754
Status Public on Oct 03, 2007
Title PL114_4 DNA
Sample type genomic
 
Channel 1
Source name Normal male genomic DNA
Organism Homo sapiens
Characteristics Normal male genomic DNA
LabeledExtract: 49668.Channel_1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name PL114_4 DNA
Organism Homo sapiens
Characteristics Prostate genomic DNA; PL114_4 DNA
Prostate genomic DNA; LabeledExtract: 49668.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 = 38.62; Parameter Scan Time = 10:39:04; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148331; 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 = 38.62; Parameter Scan Time = 10:39:04; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513234; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; 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/2004-02/49668.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
1 496 516 135 158 361 358 480 491 135 162 345 333 0 0 89 120 32 45 100 100 100 100 719 678 1.008 .992 .965 .97 1.023 1.473 32 232 1.019 .621 70 1760 6230 99 106 64 71 0 649 199 450 1.247 618 419 .802 1.214 .319 .28
2 758 557 135 161 623 396 760 560 139 166 625 399 0 0 176 178 34 47 100 100 100 100 1019 1024 1.573 .636 .638 .582 .632 1.451 32 220 .68 .822 70 1900 6230 99 106 78 85 0 701 202 498 .799 704 502 1.251 .803 -.323 -.317
3 1031 844 137 170 894 674 1134 855 138 172 997 685 0 0 301 231 32 46 98 100 98 100 1568 1682 1.326 .754 .687 .797 .744 1.705 52 278 .733 .869 80 2040 6240 100 108 92 100 0 1062 214 848 .948 1075 862 1.055 .864 -.077 -.211
4 678 477 137 164 541 313 684 484 139 166 547 320 0 0 83 96 32 46 100 100 100 100 854 867 1.728 .579 .585 .555 .556 1.361 32 171 .581 .737 60 2190 6240 101 107 108 114 0 600 206 394 .728 609 402 1.374 .736 -.459 -.443
5 1202 1015 138 172 1064 843 1176 1023 140 175 1038 851 0 0 277 356 34 46 100 98 100 96 1907 1889 1.262 .792 .82 .735 .793 1.685 52 354 .822 .838 90 2330 6230 98 107 120 129 0 1277 216 1060 .996 1287 1070 1.004 1.031 -.005 .044
6 510 466 141 174 369 292 506 439 144 177 365 265 0 0 88 119 34 44 100 100 100 100 661 630 1.264 .791 .726 .746 .816 1.666 32 170 .77 .59 60 2480 6230 100 106 137 143 0 586 219 367 .995 552 333 1.005 .913 -.007 -.131
7 957 833 133 156 824 677 966 895 136 164 833 739 0 0 189 233 34 47 100 94 100 94 1501 1572 1.217 .822 .887 .759 .842 1.776 52 333 .817 .852 90 2620 6230 98 107 149 158 0 1048 196 851 1.033 1126 929 .968 1.116 .047 .158
8 893 870 131 161 762 709 906 859 135 161 775 698 0 0 258 224 32 45 100 100 100 100 1471 1473 1.075 .93 .901 .954 .91 1.368 52 302 .904 .843 90 2770 6240 99 108 164 173 0 1094 202 892 1.17 1080 878 .855 1.133 .227 .18
9 647 659 133 161 514 498 679 673 138 163 546 512 0 0 106 133 33 44 100 100 100 100 1012 1058 1.032 .969 .938 .95 .961 1.432 52 312 1.009 .779 90 2920 6230 98 107 179 188 0 829 202 626 1.219 846 644 .821 1.179 .285 .238
10 906 741 131 152 775 589 944 771 133 156 813 619 0 0 258 293 31 42 100 93 100 92 1364 1432 1.316 .76 .761 .67 .753 1.753 80 365 .806 .855 100 3070 6230 98 108 194 204 0 932 191 741 .956 970 779 1.046 .958 -.065 -.063
11 634 539 135 153 499 386 645 535 135 156 510 382 0 0 114 126 33 45 100 100 100 98 885 892 1.293 .774 .749 .74 .738 1.55 52 262 .788 .756 80 3210 6230 99 107 209 217 0 678 192 485 .973 673 480 1.028 .942 -.04 -.086
12 785 751 136 158 649 593 781 781 138 164 645 623 0 0 137 203 35 47 100 100 100 100 1242 1268 1.094 .914 .966 .861 .963 1.555 52 284 .947 .792 80 3360 6230 99 107 224 232 0 945 199 746 1.149 982 784 .87 1.215 .201 .281
13 896 826 135 160 761 666 907 831 139 163 772 671 0 0 145 204 35 41 100 100 100 100 1427 1443 1.143 .875 .869 .842 .879 1.382 52 300 .905 .858 90 3510 6230 98 107 238 247 0 1039 201 838 1.101 1045 844 .909 1.093 .138 .129
14 1036 1106 136 174 900 932 1054 1140 140 179 918 966 0 0 210 201 32 44 100 100 100 100 1832 1884 .966 1.036 1.052 1.04 1.041 1.35 52 318 1.003 .861 90 3650 6230 98 107 252 261 0 1391 219 1172 1.302 1434 1215 .768 1.323 .381 .404
15 633 640 136 172 497 468 638 633 139 176 502 461 0 0 86 120 31 46 100 100 100 100 965 963 1.062 .942 .918 .922 .935 1.287 52 264 .968 .818 80 3800 6230 99 107 268 276 0 805 216 589 1.184 796 580 .844 1.155 .244 .208
16 1951 2034 131 166 1820 1868 1812 2014 136 169 1681 1848 0 0 656 707 34 44 100 100 100 100 3688 3529 .974 1.026 1.099 1.015 1.061 1.38 52 328 1.028 .901 90 3950 6230 98 107 282 291 0 2558 209 2349 1.291 2533 2324 .775 1.383 .368 .467
17 893 874 135 174 758 700 878 950 138 178 743 776 0 0 199 313 33 45 100 98 100 96 1458 1519 1.083 .923 1.044 .812 .916 1.712 52 254 .996 .841 80 4100 6230 99 107 298 306 0 1099 219 880 1.161 1195 976 .861 1.314 .216 .393
18 1155 1094 138 176 1017 918 1198 1131 142 177 1060 955 0 0 223 245 33 47 100 100 100 100 1935 2015 1.108 .903 .901 .89 .945 1.298 52 244 .911 .883 80 4240 6230 99 107 312 320 0 1376 221 1155 1.135 1422 1201 .881 1.133 .183 .18
19 2219 2075 135 164 2084 1911 2221 2084 139 171 2086 1920 0 0 967 990 48 49 100 100 98 98 3995 4006 1.091 .917 .92 .863 .885 2.2 80 397 .936 .874 100 4390 6230 98 108 326 336 0 2610 206 2403 1.153 2621 2415 .867 1.158 .206 .211
20 1031 858 127 176 904 682 1084 859 133 179 957 683 0 0 239 178 33 49 100 100 100 100 1586 1640 1.326 .754 .714 .753 .762 1.269 52 313 .729 .865 90 4540 6230 98 107 341 350 0 1079 221 858 .949 1080 859 1.054 .898 -.076 -.156

Total number of rows: 41664

Table truncated, full table size 9371 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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