NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM35646 Query DataSets for GSM35646
Status Public on May 27, 2005
Title array-CGH - AA2
Sample type genomic
 
Channel 1
Source name male reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name AA2
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51537.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 = 31.91; Parameter Scan Time = 15:59:52; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 84490; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.12; 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 = 31.91; Parameter Scan Time = 15:59:52; Parameter PMT Volts = 710; Parameter Scan Date = 2004-04-13; Parameter Pixel Size = 10; Parameter Laser on time = 153968; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; 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
1 506 196 310 .805 496 300 1.243 .757 -.314 -.401 507 568 122 220 385 348 518 557 123 225 396 337 0 0 135 161 20 53 100 100 100 98 733 733 1.106 .904 .851 .866 .855 1.465 53 258 .965 .88 80 1520 6320 36 44 36 44 0
2 707 185 522 .767 708 523 1.304 .75 -.383 -.415 799 794 119 208 680 586 817 796 120 211 698 588 0 0 240 211 19 51 100 100 100 100 1266 1286 1.16 .862 .842 .869 .877 1.345 51 155 .841 .94 70 1660 6310 35 42 50 57 0
3 683 185 498 .705 702 517 1.419 .721 -.505 -.471 822 767 116 208 706 559 833 789 118 215 717 581 0 0 283 227 20 59 100 100 100 100 1265 1298 1.263 .792 .81 .787 .771 1.394 65 269 .785 .94 90 1810 6310 34 43 64 73 0
4 473 194 279 .506 476 282 1.978 .492 -.984 -1.025 671 531 120 218 551 313 694 535 121 226 574 317 0 0 171 106 22 60 100 100 100 95 864 891 1.76 .568 .552 .557 .559 1.504 44 155 .548 .88 70 1960 6320 36 43 80 87 0
5 904 188 716 .836 897 709 1.196 .789 -.258 -.342 978 1016 121 211 857 805 1020 1008 121 215 899 797 0 0 303 259 21 58 100 100 100 100 1662 1696 1.065 .939 .887 .961 .934 1.275 76 338 .919 .96 100 2100 6320 35 45 93 103 0
6 536 199 336 .705 538 339 1.418 .674 -.504 -.569 599 602 122 224 477 378 625 605 124 228 503 381 0 0 170 115 21 62 100 100 100 97 855 884 1.262 .792 .757 .803 .788 1.454 40 128 .771 .92 60 2250 6310 36 42 110 116 0
7 761 186 575 .832 735 549 1.202 .83 -.265 -.27 812 855 121 209 691 646 783 826 123 216 662 617 0 0 231 232 21 61 100 100 100 100 1337 1279 1.07 .935 .932 .925 .904 1.304 71 240 .937 .96 90 2390 6310 34 43 122 131 0
8 698 184 514 .773 687 503 1.293 .713 -.371 -.487 785 784 121 207 664 577 826 772 123 211 705 565 0 0 234 217 21 56 100 100 100 100 1241 1270 1.151 .869 .801 .865 .867 1.308 64 219 .855 .94 90 2530 6320 35 44 136 145 0
9 467 196 271 .64 457 262 1.562 .623 -.643 -.683 545 525 121 220 424 305 541 514 123 225 420 294 0 0 98 111 20 58 100 98 100 98 729 714 1.39 .719 .7 .684 .704 1.497 54 207 .759 .88 80 2690 6310 35 43 153 161 0
10 1005 206 798 .922 1048 841 1.085 .912 -.117 -.133 985 1129 119 232 866 897 1041 1177 121 230 922 945 0 0 309 337 19 59 100 100 100 100 1763 1867 .965 1.036 1.025 1.036 1.023 1.308 70 220 1.026 .95 90 2830 6310 34 43 166 175 0
11 473 201 271 .684 459 258 1.462 .679 -.548 -.558 514 531 117 226 397 305 497 516 119 224 380 290 0 0 111 109 20 56 100 100 100 96 702 670 1.302 .768 .763 .742 .738 1.427 57 214 .82 .88 80 2980 6310 35 43 182 190 0
12 458 188 271 .472 452 264 2.118 .436 -1.083 -1.197 693 515 120 211 573 304 726 508 121 212 606 297 0 0 181 109 19 57 100 100 100 98 877 903 1.885 .531 .49 .53 .508 1.645 64 258 .505 .83 90 3120 6310 34 43 195 204 0
13 904 193 711 .981 935 742 1.019 .973 -.028 -.04 850 1016 125 217 725 799 888 1051 126 220 763 834 0 0 250 272 20 60 100 100 100 100 1524 1597 .907 1.102 1.093 1.108 1.087 1.213 73 233 1.094 .97 90 3270 6310 34 43 210 219 0
14 1086 201 885 1.017 1127 926 .983 1.011 .024 .015 996 1220 126 226 870 994 1042 1266 126 230 916 1040 0 0 285 296 21 61 100 100 100 100 1864 1956 .875 1.143 1.135 1.167 1.128 1.292 76 304 1.122 .96 100 3420 6310 34 44 225 235 0
15 504 203 301 .824 506 303 1.213 .801 -.279 -.321 490 566 125 228 365 338 503 568 127 233 378 340 0 0 110 122 22 64 100 100 100 96 703 718 1.08 .926 .899 .91 .925 1.514 63 215 .962 .85 90 3570 6310 34 43 240 249 0
16 1396 199 1197 .78 1320 1121 1.282 .71 -.359 -.495 1655 1569 120 224 1535 1345 1699 1483 122 222 1579 1259 0 0 767 665 21 60 100 100 100 100 2880 2838 1.141 .876 .797 .924 .889 1.429 81 229 .854 .94 90 3700 6300 33 42 253 262 0
17 965 202 763 .907 990 788 1.103 .877 -.141 -.189 962 1084 121 227 841 857 1019 1112 123 222 898 885 0 0 249 281 20 58 100 100 100 100 1698 1783 .981 1.019 .986 1.01 1.033 1.27 66 213 1.04 .96 90 3860 6310 34 43 269 278 0
18 1836 205 1631 1.259 1243 1039 .794 .887 .332 -.173 1421 2063 125 230 1296 1833 1296 1397 127 230 1171 1167 0 0 1185 2873 21 58 100 100 100 100 3129 2338 .707 1.414 .997 1.189 1.053 1.805 73 263 2.165 .9 100 4000 6310 34 44 283 293 0
19 3465 210 3255 1.223 3476 3266 .818 1.135 .291 .183 2788 3893 127 236 2661 3657 3004 3905 129 238 2877 3669 0 0 873 1107 21 61 100 100 100 100 6318 6546 .728 1.374 1.275 1.407 1.342 1.237 89 308 1.364 .98 110 4150 6310 33 44 297 308 0
20 592 198 394 .524 570 372 1.907 .484 -.931 -1.048 876 665 124 222 752 443 893 640 126 225 769 418 0 0 243 191 21 56 100 100 100 100 1195 1187 1.698 .589 .544 .573 .525 1.478 77 216 .565 .87 90 4290 6300 33 42 312 321 0

Total number of rows: 41664

Table truncated, full table size 9648 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap