NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90763 Query DataSets for GSM90763
Status Public on Jan 06, 2006
Title CHIMP 2 [HSR (human female) vs. PTD (Bonobo female)]
Sample type genomic
 
Channel 1
Source name Human female genomic DNA
Organism Homo sapiens
Characteristics Human female genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Chimpanzee female genomic DNA
Organism Homo sapiens
Characteristics Chimpanzee female genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38128.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 Jan 05, 2006
Last update date Feb 23, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL1448
Series (2)
GSE3980 Lineage-specific gene duplication and loss in human and great ape evolution
GSE9028 Extended Primate aCGH

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
1 577 542 138 172 439 370 594 554 143 173 456 382 0 0 121 151 52 56 100 100 100 96 809 838 1.186 .843 .838 .792 .864 1.59 32 189 .878 .83 70 2150 7260 82 89 59 66 0 664 211 454 1.033 679 468 .968 1.027 .047 .038
2 911 861 139 172 772 689 939 932 145 178 800 760 0 0 307 356 50 53 96 86 94 86 1461 1560 1.12 .892 .95 .805 .964 2.207 52 253 .947 .91 80 2280 7230 79 87 72 80 0 1056 211 845 1.094 1143 932 .914 1.165 .13 .22
3 176 193 138 169 38 24 148 167 140 172 10 -2 0 0 144 96 36 55 32 28 13 12 62 8 1.583 .632 null 1.162 1.283 3.871 80 406 .446 .6 100 2430 7240 79 89 86 96 -50 237 207 29 .774 205 -2 1.291 null -.369 null
4 593 484 136 143 457 341 615 454 140 163 479 311 0 0 110 168 39 60 100 100 100 100 798 790 1.34 .746 .649 .683 .695 1.609 12 94 .864 .86 50 2610 7230 80 85 106 111 0 593 175 418 .915 557 381 1.093 .796 -.128 -.329
5 1466 1129 136 165 1330 964 1418 1140 140 169 1282 975 0 0 382 375 35 51 100 100 100 100 2294 2257 1.38 .725 .761 .671 .731 1.625 32 208 .716 .91 70 2720 7240 80 87 116 123 0 1384 202 1182 .889 1398 1195 1.125 .932 -.17 -.101
6 1265 1066 139 169 1126 897 1217 1017 146 182 1078 848 0 0 454 526 52 76 100 87 100 87 2023 1926 1.255 .797 .787 .794 .779 1.846 32 220 .827 .84 70 2870 7220 78 85 131 138 0 1307 207 1100 .977 1247 1040 1.024 .964 -.034 -.052
7 764 687 138 173 626 514 819 734 141 174 681 561 0 0 323 322 33 55 96 90 96 81 1140 1242 1.218 .821 .824 .834 .873 1.723 32 146 .857 .9 60 3040 7240 81 87 149 155 0 842 212 630 1.007 900 688 .993 1.01 .01 .014
8 842 751 142 158 700 593 956 736 143 162 814 578 0 0 467 300 33 52 93 100 84 100 1293 1392 1.18 .847 .71 1.127 .899 2.553 32 191 .735 .88 70 3140 7230 79 86 158 165 0 921 194 727 1.039 902 709 .963 .871 .055 -.2
9 822 653 139 175 683 478 835 686 140 176 696 511 0 0 170 195 32 56 100 97 100 96 1161 1207 1.429 .7 .734 .622 .736 1.814 80 364 .734 .91 100 3310 7240 79 89 174 184 0 801 215 586 .858 841 626 1.165 .9 -.221 -.152
10 379 341 137 175 242 166 379 329 139 185 242 154 0 0 108 101 37 57 100 84 96 69 408 396 1.458 .686 .636 .65 .816 2.324 52 220 .655 .59 80 3440 7240 80 88 188 196 0 418 215 204 .841 403 189 1.189 .78 -.25 -.358
11 764 614 137 168 627 446 776 594 142 175 639 426 0 0 168 161 51 64 100 98 100 98 1073 1065 1.406 .711 .667 .675 .697 1.702 52 306 .678 .86 90 3590 7230 78 87 202 211 0 753 206 547 .872 728 522 1.147 .817 -.197 -.291
12 669 556 139 173 530 383 652 557 147 175 513 384 0 0 132 139 59 60 100 100 100 96 913 897 1.384 .723 .749 .684 .671 1.546 52 293 .712 .85 90 3740 7230 78 87 217 226 0 682 212 470 .886 683 471 1.129 .918 -.175 -.124
13 1316 1136 142 177 1174 959 1365 1145 156 186 1223 968 0 0 244 273 94 75 100 100 100 100 2133 2191 1.224 .817 .791 .797 .807 1.343 52 293 .818 .94 90 3880 7230 78 87 231 240 0 1393 217 1176 1.001 1404 1187 .999 .97 .002 -.043
14 1024 677 142 170 882 507 1043 697 153 179 901 527 0 0 315 218 83 67 100 97 100 96 1389 1428 1.74 .575 .585 .547 .559 1.663 80 406 .562 .88 100 4040 7230 78 88 247 257 0 830 208 622 .705 855 646 1.419 .717 -.505 -.48
15 677 490 148 177 529 313 680 491 162 190 532 314 0 0 110 84 80 82 100 100 100 98 842 846 1.69 .592 .59 .582 .585 1.41 52 257 .614 .84 90 4180 7230 78 87 261 270 0 601 217 384 .725 602 385 1.379 .724 -.463 -.467
16 206 232 147 181 59 51 151 196 155 191 4 15 0 0 289 229 70 83 12 21 3 5 110 19 1.157 .864 3.75 2.252 1.866 4.36 80 358 .824 .86 100 4320 7230 78 88 275 285 -50 284 222 63 1.06 240 18 .944 4.597 .084 2.201
17 1496 1358 146 166 1350 1192 1502 1366 155 183 1356 1200 0 0 244 256 73 88 100 100 100 100 2542 2556 1.133 .883 .885 .873 .898 1.294 52 277 .879 .94 90 4470 7230 78 87 290 299 0 1665 204 1461 1.083 1675 1471 .924 1.085 .114 .118
18 144 175 150 186 -6 -11 139 167 158 195 -11 -19 0 0 30 65 68 84 3 7 0 2 -17 -30 null null null 1.793 2.193 3.388 80 339 1.276 .52 100 4610 7230 78 88 304 314 -50 215 228 -13 null 205 -23 null null null null
19 3039 2365 149 188 2890 2177 3093 2426 162 197 2944 2238 0 0 511 513 130 94 100 100 100 100 5067 5182 1.328 .753 .76 .736 .737 1.356 52 288 .736 .95 90 4760 7230 78 87 319 328 0 2899 230 2669 .924 2974 2744 1.083 .932 -.115 -.102
20 743 484 146 178 597 306 741 484 162 188 595 306 0 0 122 98 128 91 100 100 100 92 903 901 1.951 .513 .514 .498 .51 1.478 52 301 .54 .84 90 4910 7230 78 87 334 343 0 593 218 375 .628 593 375 1.591 .631 -.67 -.665

Total number of rows: 43104

Table truncated, full table size 9813 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap