NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM35649 Query DataSets for GSM35649
Status Public on May 27, 2005
Title array-CGH - AO2
Sample type genomic
 
Channel 1
Source name female reference
Organism Homo sapiens
Extracted molecule genomic DNA
 
Channel 2
Source name AO2
Organism Homo sapiens
Extracted molecule genomic DNA
 
 
Description Simple annotation: tumor, Brain
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2004-04/51506.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 = 31.79; Parameter Scan Time = 15:52:33; Parameter PMT Volts = 530; Parameter Scan Date = 2004-03-26; Parameter Pixel Size = 10; Parameter Laser on time = 80676; 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 = 31.79; Parameter Scan Time = 15:52:33; Parameter PMT Volts = 710; Parameter Scan Date = 2004-03-26; Parameter Pixel Size = 10; Parameter Laser on time = 150134; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.48; 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
1 969 290 679 .83 990 700 1.205 .815 -.269 -.294 988 982 170 294 818 688 1028 1003 175 298 858 709 0 0 257 225 33 70 100 100 100 100 1506 1567 1.189 .841 .826 .84 .844 1.227 69 279 .852 .95 90 1950 6720 31 40 22 31 0
2 1092 295 797 .663 1128 833 1.508 .661 -.592 -.596 1375 1107 173 299 1202 808 1432 1143 178 305 1259 844 0 0 347 253 33 73 100 100 100 100 2010 2103 1.488 .672 .67 .668 .656 1.22 62 225 .665 .96 90 2100 6720 31 40 37 46 0
3 1094 308 786 .521 1078 770 1.92 .483 -.941 -1.049 1679 1109 169 312 1510 797 1762 1092 172 312 1593 780 0 0 539 315 27 74 100 100 100 100 2307 2373 1.895 .528 .49 .522 .523 1.33 78 293 .524 .95 100 2240 6720 31 41 51 61 0
4 553 310 243 .335 538 228 2.987 .322 -1.579 -1.635 895 560 170 314 725 246 878 545 173 327 708 231 0 0 138 153 28 82 100 88 100 69 971 939 2.947 .339 .326 .294 .338 1.855 43 145 .38 .73 70 2380 6720 32 39 66 73 0
5 627 313 314 .327 601 288 3.059 .3 -1.613 -1.736 1132 635 172 317 960 318 1132 609 174 325 960 292 0 0 216 172 30 80 100 95 100 86 1278 1252 3.019 .331 .304 .298 .301 1.808 87 347 .323 .78 110 2530 6720 30 41 79 90 0
6 882 325 557 .754 870 546 1.326 .715 -.407 -.484 910 894 171 329 739 565 934 882 173 330 763 553 0 0 170 151 28 71 100 100 100 100 1304 1316 1.308 .765 .725 .76 .75 1.354 50 190 .786 .91 80 2680 6720 32 40 96 104 0
7 1051 315 736 .713 994 679 1.402 .636 -.487 -.652 1205 1065 173 319 1032 746 1240 1007 175 318 1067 688 0 0 284 278 32 77 100 100 100 100 1778 1755 1.383 .723 .645 .721 .693 1.563 88 251 .751 .79 100 2830 6720 31 41 110 120 0
8 1174 315 859 .631 1172 857 1.584 .603 -.663 -.731 1544 1190 183 319 1361 871 1606 1188 188 332 1423 869 0 0 310 226 44 97 100 100 100 100 2232 2292 1.563 .64 .611 .636 .623 1.291 76 261 .626 .95 100 2970 6720 31 41 124 134 0
9 783 338 445 .357 771 432 2.798 .348 -1.484 -1.524 1432 794 187 343 1245 451 1430 781 241 427 1243 438 0 0 224 205 124 222 100 86 100 48 1696 1681 2.761 .362 .352 .318 .368 1.811 52 211 .351 .74 80 3120 6710 31 39 140 148 -50
10 1412 330 1082 .609 1267 937 1.641 .52 -.714 -.944 1951 1431 175 334 1776 1097 1978 1284 220 402 1803 950 0 0 590 509 122 214 100 100 100 98 2873 2753 1.619 .618 .527 .598 .582 1.32 81 288 .63 .92 100 3260 6710 30 40 153 163 0
11 896 316 580 .817 872 557 1.224 .778 -.291 -.362 882 908 172 320 710 588 887 884 174 325 715 564 0 0 169 205 31 79 100 100 100 100 1298 1279 1.207 .828 .789 .805 .822 1.358 70 274 .872 .92 100 3410 6720 31 41 168 178 0
12 959 314 645 .693 920 606 1.443 .636 -.529 -.654 1110 972 179 318 931 654 1132 932 180 329 953 614 0 0 208 189 29 74 100 100 100 100 1585 1567 1.424 .702 .644 .691 .68 1.248 68 223 .691 .93 90 3550 6720 31 40 182 191 0
13 918 323 595 .401 887 564 2.494 .367 -1.319 -1.446 1668 930 184 327 1484 603 1722 899 187 341 1538 572 0 0 310 178 38 84 100 100 100 100 2087 2110 2.461 .406 .372 .4 .389 1.289 83 272 .379 .9 100 3700 6710 30 40 197 207 0
14 1781 334 1448 .875 1789 1455 1.143 .824 -.193 -.28 1840 1805 185 338 1655 1467 1952 1813 190 352 1767 1475 0 0 454 386 43 96 100 100 100 100 3122 3242 1.128 .886 .835 .892 .88 1.199 87 300 .87 .97 110 3840 6710 29 40 210 221 0
15 948 334 615 .792 926 592 1.262 .725 -.336 -.465 964 961 188 338 776 623 1005 938 196 364 817 600 0 0 186 169 58 107 100 100 100 100 1399 1417 1.246 .803 .734 .802 .777 1.35 85 200 .783 .9 90 3990 6700 29 38 226 235 0
16 2831 329 2502 .774 2621 2292 1.293 .716 -.37 -.482 3419 2869 184 333 3235 2536 3385 2656 191 345 3201 2323 0 0 1302 1191 53 102 100 100 100 100 5771 5524 1.276 .784 .726 .768 .738 1.304 84 252 .799 .97 100 4140 6710 30 40 241 251 0
17 1791 331 1460 .905 1844 1514 1.105 .898 -.143 -.156 1798 1815 185 335 1613 1480 1871 1869 190 336 1686 1534 0 0 376 357 35 83 100 100 100 100 3093 3220 1.09 .918 .91 .917 .898 1.184 78 253 .912 .97 100 4280 6710 30 40 255 265 0
18 1956 344 1611 .809 1995 1651 1.236 .797 -.306 -.326 2185 1982 193 349 1992 1633 2263 2022 199 353 2070 1673 0 0 470 452 41 85 100 100 100 100 3625 3743 1.22 .82 .808 .81 .829 1.22 75 237 .815 .97 100 4430 6710 30 40 270 280 0
19 5664 360 5304 1.206 5608 5247 .829 1.157 .271 .21 4599 5740 203 365 4396 5375 4738 5683 204 369 4535 5318 0 0 1249 1652 39 84 100 100 100 100 9771 9853 .818 1.223 1.173 1.228 1.194 1.238 105 258 1.231 .98 110 4570 6710 29 40 283 294 0
20 1070 329 741 .573 993 664 1.746 .491 -.804 -1.026 1477 1084 183 333 1294 751 1535 1006 185 340 1352 673 0 0 297 237 36 79 100 100 100 100 2045 2025 1.723 .58 .498 .573 .573 1.299 88 231 .566 .93 100 4720 6710 30 40 299 309 0

Total number of rows: 41664

Table truncated, full table size 9673 Kbytes.




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