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Sample GSM35659 Query DataSets for GSM35659
Status Public on May 27, 2005
Title array-CGH - GBM11
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name GBM11
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51550.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 = 33.80; Parameter Scan Time = 19:10:39; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 84680; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.10; 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 = 33.80; Parameter Scan Time = 19:10:39; Parameter PMT Volts = 720; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 154158; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; 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
1 844 293 551 1.068 835 542 .936 .993 .095 -.009 655 885 139 307 516 578 685 876 141 305 546 569 0 0 235 274 22 78 100 100 100 100 1094 1115 .893 1.12 1.042 1.143 1.178 1.444 61 307 1.173 .91 90 1430 5670 26 35 26 35 0
2 962 296 665 .728 973 677 1.374 .659 -.458 -.602 1056 1009 142 311 914 698 1169 1021 141 316 1027 710 0 0 368 201 22 83 100 100 100 100 1612 1737 1.309 .764 .691 .827 .767 1.575 55 226 .703 .91 80 1590 5660 26 34 43 51 0
3 1028 318 709 .648 1036 718 1.542 .622 -.625 -.685 1241 1078 147 334 1094 744 1301 1087 152 339 1154 753 0 0 359 251 27 84 100 100 100 100 1838 1907 1.47 .68 .653 .685 .666 1.467 69 215 .654 .91 80 1730 5660 26 34 57 65 0
4 766 328 439 .648 751 423 1.544 .606 -.627 -.724 834 804 157 344 677 460 856 788 158 352 699 444 0 0 199 162 30 90 100 97 100 97 1137 1143 1.472 .679 .635 .664 .676 1.778 40 163 .662 .82 70 1880 5660 26 33 72 79 0
5 1183 314 869 .696 1245 931 1.437 .66 -.523 -.6 1398 1241 149 329 1249 912 1561 1306 151 328 1412 977 0 0 433 298 26 74 100 100 100 100 2161 2389 1.37 .73 .692 .742 .711 1.504 81 252 .708 .94 90 2010 5660 25 34 84 93 0
6 736 302 434 .82 723 420 1.22 .745 -.286 -.424 679 772 150 317 529 455 714 758 153 318 564 441 0 0 187 144 24 73 100 100 100 97 984 1005 1.163 .86 .782 .874 .868 1.452 45 154 .831 .86 70 2170 5660 26 33 101 108 0
7 903 309 594 .763 896 587 1.31 .726 -.39 -.462 925 947 147 324 778 623 956 940 151 326 809 616 0 0 239 180 26 80 100 100 100 100 1401 1425 1.249 .801 .761 .816 .779 1.578 70 323 .787 .88 100 2310 5660 25 35 114 124 0
8 1043 335 708 .886 1054 720 1.128 .862 -.174 -.214 957 1094 158 351 799 743 993 1106 157 351 835 755 0 0 310 263 26 82 100 100 100 100 1542 1590 1.075 .93 .904 .947 .895 1.517 72 195 .904 .92 80 2460 5650 25 33 130 138 0
9 885 326 559 .724 888 562 1.382 .742 -.467 -.431 930 928 158 342 772 586 915 931 161 347 757 589 0 0 288 215 45 81 100 100 100 98 1358 1346 1.317 .759 .778 .752 .779 1.441 60 207 .751 .89 90 2610 5660 25 34 144 153 0
10 1201 317 884 .869 1174 856 1.151 .789 -.203 -.342 1171 1260 154 333 1017 927 1239 1231 157 335 1085 898 0 0 548 383 38 82 100 100 100 98 1944 1983 1.097 .912 .828 1.019 .92 1.599 91 301 .844 .94 110 2750 5660 24 35 157 168 0
11 781 318 462 .699 767 449 1.43 .655 -.516 -.609 817 819 156 334 661 485 841 805 158 339 685 471 0 0 176 164 28 82 100 100 100 100 1146 1156 1.363 .734 .688 .72 .756 1.43 56 254 .751 .89 90 2900 5660 25 34 173 182 0
12 958 317 641 .764 961 643 1.308 .735 -.387 -.445 992 1005 154 333 838 672 1030 1008 156 338 876 675 0 0 209 185 27 80 100 100 100 100 1510 1551 1.247 .802 .771 .797 .812 1.281 56 224 .783 .93 80 3050 5660 26 34 189 197 0
13 1370 321 1049 .967 1440 1119 1.034 .957 -.048 -.063 1238 1437 154 337 1084 1100 1323 1511 155 346 1169 1174 0 0 358 374 26 83 100 100 100 100 2184 2343 .985 1.015 1.004 1.02 .997 1.4 71 222 1.011 .95 90 3190 5660 25 34 202 211 0
14 1436 344 1092 .853 1481 1137 1.172 .838 -.229 -.255 1440 1506 161 361 1279 1145 1518 1554 163 367 1357 1193 0 0 369 326 30 86 100 100 100 100 2424 2550 1.117 .895 .879 .9 .9 1.349 72 240 .887 .94 90 3340 5650 24 33 217 226 0
15 656 349 307 .83 656 307 1.205 .787 -.269 -.345 532 688 162 366 370 322 552 688 167 368 390 322 0 0 109 131 30 89 100 97 98 83 692 712 1.149 .87 .826 .837 .805 1.996 71 197 1.008 .7 90 3490 5650 24 33 232 241 0
16 3167 334 2833 .869 3254 2920 1.151 .822 -.203 -.282 3420 3322 158 350 3262 2972 3709 3413 159 355 3551 3063 0 0 1653 1217 30 92 100 100 100 100 6234 6614 1.098 .911 .863 .99 .9 1.44 81 268 .855 .97 100 3630 5660 25 35 246 256 0
17 3780 338 3441 1.64 1559 1220 .61 .922 .713 -.117 2258 3965 159 355 2099 3610 1482 1635 161 363 1323 1280 0 0 2511 6691 34 89 100 100 100 100 5709 2603 .581 1.72 .967 1.133 .981 1.793 75 214 2.766 .81 90 3770 5660 25 34 260 269 0
18 1652 347 1305 .841 1742 1395 1.189 .841 -.25 -.249 1706 1733 154 364 1552 1369 1812 1827 158 366 1658 1463 0 0 422 413 29 89 100 100 100 100 2921 3121 1.134 .882 .882 .875 .878 1.259 61 173 .866 .96 80 3920 5660 26 34 276 284 0
19 3602 335 3267 1.023 3717 3382 .977 .871 .033 -.2 3346 3778 153 351 3193 3427 4037 3899 155 358 3884 3548 0 0 1648 1294 28 81 100 100 100 100 6620 7432 .932 1.073 .913 1.203 1.066 1.498 117 375 .996 .96 120 4070 5650 23 35 289 301 0
20 1040 318 722 .723 1009 690 1.383 .659 -.468 -.603 1142 1091 144 334 998 757 1192 1058 145 337 1048 724 0 0 291 269 26 73 100 100 100 100 1755 1772 1.318 .759 .691 .745 .725 1.353 69 208 .758 .92 90 4220 5650 24 33 305 314 0

Total number of rows: 41664

Table truncated, full table size 9620 Kbytes.




Supplementary data files not provided
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