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Sample GSM35661 Query DataSets for GSM35661
Status Public on May 27, 2005
Title array-CGH - GBM13
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name GBM13
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-05/51559.gif; format: GIF
Label_ch1 = Cy3
Label_ch2 = Cy5
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 = 32.22; Parameter Scan Time = 16:43:24; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 85330; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
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 = 32.22; Parameter Scan Time = 16:43:24; Parameter PMT Volts = 710; Parameter Scan Date = 2004-04-16; Parameter Pixel Size = 10; Parameter Laser on time = 154807; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Markus,,Bredel
 
Submission date Nov 19, 2004
Last update date May 29, 2005
Contact name Markus Bredel
E-mail(s) mbredel@stanford.edu
Phone 650-498-6012
Organization name Stanford University School of Medicine
Street address
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1715
Series (1)
GSE1991 Array-CGH in human glial brain tumors

Data table header descriptions
ID_REF ID_REF
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
VALUE 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
LOG_RAT2N_MEDIAN 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
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

Data table
ID_REF CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN VALUE LOG_RAT2N_MEDIAN 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
1 641 348 293 .767 610 263 1.304 .668 -.382 -.582 528 588 146 319 382 269 539 560 150 327 393 241 0 0 116 127 32 88 100 92 100 77 651 634 1.42 .704 .613 .656 .642 1.95 71 387 .754 .69 100 1640 5720 39 49 31 41 0
2 906 366 540 .696 851 485 1.436 .581 -.522 -.783 922 832 146 336 776 496 980 781 151 344 834 445 0 0 278 228 32 81 100 100 100 100 1272 1279 1.565 .639 .534 .64 .619 1.561 62 238 .635 .87 90 1780 5720 39 48 45 54 0
3 1096 346 750 .814 1106 759 1.229 .772 -.297 -.374 1068 1006 147 318 921 688 1131 1015 150 331 984 697 0 0 279 222 29 74 100 100 100 100 1609 1681 1.339 .747 .708 .745 .72 1.378 76 326 .726 .93 100 1930 5720 39 49 60 70 0
4 686 353 333 .516 669 316 1.938 .475 -.954 -1.074 790 630 144 324 646 306 809 614 148 330 665 290 0 0 127 109 25 76 100 100 100 95 952 955 2.111 .474 .436 .455 .468 1.48 41 149 .44 .78 70 2080 5720 40 47 76 83 0
5 1484 354 1130 .85 1470 1116 1.176 .793 -.234 -.335 1472 1362 143 325 1329 1037 1550 1349 143 327 1407 1024 0 0 374 270 22 79 100 100 100 100 2366 2431 1.282 .78 .728 .792 .788 1.26 88 319 .764 .96 100 2220 5720 39 49 89 99 0
6 605 348 257 .566 606 258 1.766 .545 -.82 -.876 598 555 144 319 454 236 618 556 145 319 474 237 0 0 101 113 23 67 100 94 100 81 690 711 1.924 .52 .5 .494 .516 1.83 38 161 .506 .64 70 2370 5720 40 47 105 112 0
7 1214 356 857 .947 1213 856 1.056 .901 -.078 -.15 1051 1114 146 327 905 787 1096 1113 148 329 950 786 0 0 217 204 24 71 100 100 100 100 1692 1736 1.15 .87 .827 .872 .853 1.302 79 286 .869 .94 100 2520 5720 39 49 119 129 0
8 1361 367 994 1.079 1373 1006 .927 1.011 .109 .015 1071 1249 150 337 921 912 1145 1260 151 341 995 923 0 0 228 237 26 77 100 100 100 100 1833 1918 1.01 .99 .928 .994 .963 1.268 73 253 .991 .96 100 2660 5720 39 49 133 143 0
9 840 345 495 .762 825 479 1.312 .733 -.392 -.448 798 771 149 317 649 454 803 757 151 328 654 440 0 0 135 151 26 81 100 100 100 100 1103 1094 1.43 .7 .673 .677 .678 1.433 71 218 .709 .85 90 2800 5710 38 47 147 156 0
10 1215 368 846 .813 1190 821 1.23 .747 -.298 -.421 1194 1115 153 338 1041 777 1253 1092 158 343 1100 754 0 0 299 212 29 90 100 100 100 100 1818 1854 1.34 .746 .685 .757 .739 1.317 73 217 .695 .92 90 2950 5710 38 47 162 171 0
11 593 364 229 .417 588 224 2.395 .41 -1.26 -1.288 699 544 151 334 548 210 699 540 154 348 548 206 0 0 100 84 29 99 100 94 100 52 758 754 2.61 .383 .376 .374 .375 1.532 59 230 .379 .6 90 3100 5720 39 48 177 186 0
12 826 367 459 .593 823 455 1.688 .576 -.755 -.797 924 758 150 337 774 421 941 755 152 349 791 418 0 0 230 135 24 84 100 98 100 97 1195 1209 1.838 .544 .528 .539 .526 1.59 71 233 .491 .83 90 3240 5720 39 48 191 200 0
13 1008 351 657 .791 994 643 1.265 .72 -.339 -.474 975 925 144 322 831 603 1037 912 144 333 893 590 0 0 226 150 21 74 100 100 100 100 1434 1483 1.378 .726 .661 .736 .738 1.304 81 283 .688 .93 100 3390 5710 38 48 206 216 0
14 1483 371 1111 1.055 1526 1155 .948 1.073 .078 .102 1202 1361 149 341 1053 1020 1225 1401 151 351 1076 1060 0 0 272 274 24 74 100 100 100 100 2073 2136 1.032 .969 .985 .966 .948 1.244 86 286 .95 .96 100 3540 5710 38 48 221 231 0
15 708 385 324 .693 680 295 1.443 .631 -.529 -.665 625 650 158 353 467 297 626 624 160 361 468 271 0 0 73 128 29 83 100 98 100 85 764 739 1.572 .636 .579 .581 .62 1.665 63 218 .671 .74 90 3690 5710 38 47 236 245 0
16 2555 383 2171 1.129 2142 1758 .886 .854 .175 -.228 2075 2345 152 352 1923 1993 2211 1966 156 352 2059 1614 0 0 683 2516 29 86 100 100 100 100 3916 3673 .965 1.036 .784 .897 .82 1.484 76 305 2.108 .69 100 3830 5710 38 48 250 260 0
17 1116 375 741 .795 1120 745 1.258 .754 -.331 -.407 1087 1024 155 344 932 680 1143 1028 157 346 988 684 0 0 226 172 27 80 100 100 100 100 1612 1672 1.371 .73 .692 .731 .713 1.274 74 290 .721 .94 100 3980 5710 38 48 265 275 0
18 1356 381 975 .929 1356 975 1.077 .853 -.107 -.229 1208 1245 158 350 1050 895 1301 1245 159 353 1143 895 0 0 265 221 27 77 100 100 100 100 1945 2038 1.173 .852 .783 .862 .851 1.268 75 259 .831 .95 100 4130 5710 38 48 280 290 0
19 4190 373 3817 1.324 4120 3748 .755 1.218 .405 .284 3031 3846 148 342 2883 3504 3226 3782 152 348 3078 3440 0 0 789 973 27 77 100 100 100 100 6387 6518 .823 1.215 1.118 1.229 1.176 1.244 92 247 1.205 .97 100 4270 5710 38 48 294 304 0
20 1095 362 733 .913 1095 733 1.095 .877 -.131 -.189 951 1005 148 332 803 673 984 1005 150 330 836 673 0 0 177 169 28 67 100 100 100 100 1476 1509 1.193 .838 .805 .835 .836 1.292 78 224 .82 .93 90 4410 5700 37 46 308 317 0

Total number of rows: 41664

Table truncated, full table size 9504 Kbytes.




Supplementary data files not provided
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