NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM229025 Query DataSets for GSM229025
Status Public on Feb 24, 2012
Title Expt. #8.4-Baboon
Sample type genomic
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Test
Organism Papio hamadryas
Characteristics Test
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Comparative genomics, DNA
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 Sep 12, 2007
Last update date Feb 24, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL5846
Series (1)
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
1 788 364 216 216 572 148 825 344 215 221 609 128 0 0 200 118 40 78 100 65 100 42 720 737 3.865 .259 .21 .31 .28 .29 26 495 .47 .94 50 2090 6420 83 88 66 71 0 455 270 185 .324 430 160 3.091 .263 -1.628 -1.928
2 867 540 213 212 654 328 829 531 214 219 616 319 0 0 235 272 40 75 100 77 100 77 982 935 1.994 .502 .518 .63 .55 .46 26 451 .66 .89 50 2230 6430 84 89 80 85 0 675 265 410 .627 664 399 1.594 .648 -.673 -.627
3 996 582 215 214 781 368 1110 566 218 223 895 352 0 0 498 283 44 78 94 78 91 75 1149 1247 2.122 .471 .393 1.27 .51 2.01 32 428 .6 .91 60 2380 6430 84 90 95 101 0 728 268 460 .589 708 440 1.697 .492 -.763 -1.024
4 799 340 216 208 583 132 847 297 217 217 631 89 0 0 183 124 45 75 100 58 100 35 715 720 4.417 .226 .141 .28 .16 .34 26 445 .46 .91 50 2520 6420 83 88 109 114 0 425 260 165 .283 371 111 3.532 .176 -1.82 -2.503
5 787 358 213 217 574 141 772 353 214 224 559 136 0 0 148 113 41 92 100 69 100 38 715 695 4.071 .246 .243 .27 .23 .16 26 455 .5 .95 50 2650 6420 83 88 122 127 0 448 271 176 .307 441 170 3.255 .304 -1.703 -1.717
6 1144 553 208 221 936 332 1162 596 209 228 954 375 0 0 238 186 41 78 100 86 100 81 1268 1329 2.819 .355 .393 .35 .38 .17 21 493 .51 .95 50 2800 6420 83 88 137 142 0 692 276 415 .444 745 469 2.255 .492 -1.173 -1.025
7 812 597 204 225 608 372 847 554 208 233 643 329 0 0 426 332 43 80 88 85 88 73 980 972 1.634 .612 .512 4.54 .52 11.14 26 451 .77 .89 50 2950 6430 84 89 152 157 0 747 281 465 .765 693 411 1.307 .64 -.386 -.644
8 868 447 204 224 664 223 909 415 208 231 705 191 0 0 266 156 42 80 100 85 96 54 887 896 2.978 .336 .271 .68 .25 1.28 26 430 .53 .88 50 3090 6430 84 89 166 171 0 559 280 279 .42 519 239 2.381 .339 -1.252 -1.562
9 501 434 208 225 293 209 503 451 210 230 295 226 0 0 159 119 42 73 91 82 89 75 502 521 1.402 .713 .766 1.16 .67 1.87 44 429 .88 .93 70 3240 6430 83 90 180 187 0 543 281 261 .892 564 283 1.121 .958 -.165 -.062
10 864 749 207 219 657 530 877 736 211 226 670 517 0 0 307 315 42 76 97 92 95 89 1187 1187 1.24 .807 .772 1.07 .79 1.32 37 423 .87 .95 70 3400 6400 80 87 196 203 0 937 274 663 1.009 920 647 .991 .965 .013 -.051
11 398 245 201 216 197 29 393 236 207 221 192 20 0 0 74 85 41 75 99 27 96 8 226 212 6.793 .147 .104 .49 .33 .52 97 389 .63 .5 110 3540 6390 77 88 208 219 0 306 270 36 .184 295 25 5.432 .13 -2.442 -2.941
12 810 569 200 221 610 348 843 589 202 228 643 368 0 0 268 199 41 75 97 88 94 82 958 1011 1.753 .57 .572 1.11 .57 2.15 34 429 .72 .93 60 3700 6390 80 86 227 233 0 712 276 435 .713 737 460 1.402 .716 -.487 -.483
13 552 429 210 224 342 205 533 451 211 232 323 227 0 0 209 145 43 81 97 82 94 65 547 550 1.668 .599 .703 1.98 .57 6.53 34 449 .79 .93 60 3840 6390 80 86 241 247 0 536 280 256 .75 564 284 1.334 .879 -.416 -.186
14 1122 874 217 233 905 641 1065 831 217 237 848 598 0 0 334 348 41 79 100 95 100 93 1546 1446 1.412 .708 .705 .81 .68 .71 44 450 .8 .96 70 3990 6400 80 87 255 262 0 1093 291 802 .886 1039 748 1.129 .882 -.175 -.181
15 474 351 216 237 258 114 506 335 213 246 290 98 0 0 142 84 42 80 92 68 89 19 372 388 2.263 .442 .338 .79 .36 1.3 37 446 .76 .92 70 4130 6400 80 87 269 276 0 439 296 143 .553 419 123 1.81 .423 -.856 -1.243
16 1625 1650 216 233 1409 1417 1741 1808 216 242 1525 1575 0 0 805 773 45 80 100 100 100 96 2826 3100 .994 1.006 1.033 1.61 .95 1.92 26 472 1.02 .94 50 4280 6400 81 86 285 290 0 2063 291 1772 1.258 2261 1970 .795 1.291 .331 .369
17 674 528 217 235 457 293 725 537 219 243 508 302 0 0 213 177 44 82 90 87 87 84 750 810 1.56 .641 .594 .91 .62 1.19 31 463 .81 .94 60 4420 6400 81 87 299 305 0 660 294 366 .802 672 378 1.247 .743 -.319 -.428
18 701 550 211 246 490 304 747 553 212 250 536 307 0 0 229 212 40 80 95 84 93 77 794 843 1.612 .62 .573 1.18 .62 2.44 44 429 .8 .92 70 4560 6400 80 87 312 319 0 688 308 380 .776 692 384 1.289 .716 -.366 -.481
19 2435 2027 210 243 2225 1784 2492 2222 214 251 2282 1979 0 0 657 679 46 84 100 100 100 98 4009 4261 1.247 .802 .867 .83 .88 .31 44 418 .86 .97 70 4710 6400 80 87 327 334 0 2535 304 2231 1.003 2779 2475 .997 1.084 .004 .117
20 743 664 212 228 531 436 754 683 212 242 542 455 0 0 152 170 43 81 100 95 100 93 967 997 1.218 .821 .839 .85 .81 .43 44 437 .92 .97 70 4860 6400 80 87 342 349 0 830 285 545 1.027 854 569 .974 1.05 .038 .07

Total number of rows: 43008

Table truncated, full table size 9467 Kbytes.




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