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Sample GSM90767 Query DataSets for GSM90767
Status Public on Jan 06, 2006
Title CHIMP 3 [HSR (human female) vs. PTF (Chimp 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/2002-10/33960.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 GPL3310
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
1 889 2413 368 504 521 1909 841 1194 373 540 473 690 0 0 267 4620 83 231 98 88 96 78 2430 1163 .273 3.664 1.459 1.827 1.445 3.209 52 255 33.458 .27 80 2120 7310 51 59 40 48 0 2343 489 1853 3.557 1159 670 .281 1.416 1.831 .502
2 1397 2480 383 528 1014 1952 1299 2147 387 547 916 1619 0 0 448 1356 93 203 100 96 100 92 2966 2535 .519 1.925 1.767 1.641 1.672 2.129 52 312 2.644 .76 90 2270 7310 50 59 54 63 -100 2408 513 1895 1.869 2084 1572 .535 1.716 .902 .779
3 2002 2522 413 518 1589 2004 2199 2154 416 531 1786 1636 0 0 569 1375 89 177 100 100 100 100 3593 3422 .793 1.261 .916 1.128 .957 1.794 12 68 2.371 .6 40 2440 7300 52 56 74 78 -100 2449 503 1946 1.224 2091 1588 .817 .889 .292 -.169
4 1302 2703 398 557 904 2146 1383 2077 413 576 985 1520 0 0 375 2039 95 202 96 96 90 90 3050 2505 .421 2.374 1.543 2.131 1.86 2.17 32 159 4.504 .69 60 2570 7310 52 58 86 92 -100 2624 541 2083 2.305 2017 1476 .434 1.498 1.205 .583
5 2130 2710 381 560 1749 2150 2107 2368 393 582 1726 1808 0 0 598 1191 92 187 100 100 100 100 3899 3534 .813 1.229 1.048 1.185 1.07 1.989 52 317 1.535 .74 90 2710 7300 49 58 98 107 0 2631 544 2087 1.193 2299 1755 .838 1.017 .255 .024
6 1445 2154 383 539 1062 1615 1450 2072 390 575 1067 1533 0 0 418 757 91 190 98 100 98 100 2677 2600 .658 1.521 1.437 1.568 1.549 2.101 52 239 2.452 .7 80 2850 7310 51 59 113 121 0 2091 523 1568 1.476 2012 1488 .677 1.395 .562 .48
7 1854 2402 381 534 1473 1868 1911 2227 383 573 1530 1693 0 0 877 1160 89 202 92 96 90 94 3341 3223 .789 1.268 1.107 1.273 1.229 2.246 52 267 1.39 .79 80 3010 7300 50 58 129 137 0 2332 518 1814 1.231 2162 1644 .812 1.074 .3 .103
8 1366 1895 402 606 964 1289 1401 1827 421 663 999 1221 0 0 373 582 164 308 100 100 96 90 2253 2220 .748 1.337 1.222 1.315 1.24 1.85 32 183 1.79 .74 70 3130 7300 50 57 141 148 0 1840 588 1251 1.298 1774 1185 .77 1.187 .377 .247
9 1378 2119 390 593 988 1526 1339 1837 406 628 949 1244 0 0 374 1243 131 250 100 98 98 96 2514 2193 .647 1.545 1.311 1.35 1.22 2.13 80 409 2.759 .6 100 3280 7300 49 59 155 165 0 2057 576 1482 1.5 1783 1208 .667 1.273 .585 .348
10 1045 2220 415 559 630 1661 1088 1657 415 592 673 1098 0 0 351 1263 104 196 84 96 84 93 2291 1771 .379 2.637 1.632 2.549 2.267 2.372 32 142 3.832 .66 60 3440 7310 52 58 173 179 0 2155 543 1613 2.56 1609 1066 .391 1.584 1.356 .664
11 1332 2066 397 584 935 1482 1333 1696 398 616 936 1112 0 0 327 1337 100 225 100 100 100 98 2417 2048 .631 1.585 1.188 1.362 1.235 1.905 80 388 3.007 .6 110 3580 7300 48 59 184 195 -100 2006 567 1439 1.539 1647 1080 .65 1.153 .622 .206
12 1331 2047 377 579 954 1468 1262 1785 387 615 885 1206 0 0 418 1003 103 231 100 98 100 95 2422 2091 .65 1.539 1.363 1.413 1.422 1.813 80 335 2.146 .7 100 3720 7300 49 59 199 209 -100 1987 562 1425 1.494 1733 1171 .669 1.323 .579 .404
13 1368 2516 362 549 1006 1967 1239 1934 370 574 877 1385 0 0 486 1740 92 197 100 100 98 97 2973 2262 .511 1.955 1.579 1.683 1.633 1.681 80 318 2.977 .77 100 3870 7300 49 59 214 224 -100 2443 533 1910 1.898 1878 1345 .527 1.533 .925 .617
14 1655 1695 360 516 1295 1179 1684 1598 364 531 1324 1082 0 0 405 536 92 186 98 100 98 99 2474 2406 1.098 .91 .817 .878 .827 1.643 120 376 1.2 .73 120 4020 7300 48 60 228 240 0 1646 501 1145 .884 1551 1050 1.131 .793 -.178 -.334
15 1156 2144 363 526 793 1618 1185 1690 366 547 822 1164 0 0 401 1549 89 237 90 94 88 87 2411 1986 .49 2.04 1.416 1.67 1.388 2.364 120 368 4.281 .57 120 4160 7300 48 60 242 254 -100 2082 511 1571 1.981 1641 1130 .505 1.375 .986 .459
16 4262 4554 343 483 3919 4071 4072 4501 357 513 3729 4018 0 0 1459 1285 117 204 98 100 98 100 7990 7747 .963 1.039 1.078 1.082 1.015 1.674 120 415 1.01 .93 120 4310 7300 48 60 257 269 0 4421 469 3952 1.009 4370 3901 .992 1.046 .012 .065
17 2010 2669 333 448 1677 2221 2070 2698 1478 1458 1737 2250 0 0 738 990 5355 4640 0 0 0 0 3898 3987 .755 1.324 1.295 1.362 1.28 1.879 120 482 .854 .9 130 4460 7300 47 60 271 284 0 2591 435 2156 1.286 2619 2184 .778 1.258 .363 .331
18 639 614 362 485 277 129 397 535 3194 3019 35 50 0 0 1025 414 8220 7102 0 0 0 0 406 85 2.147 .466 1.429 1.167 1.556 3.288 52 191 .452 .76 80 4610 7290 49 57 289 297 -100 596 471 125 .452 519 49 2.212 1.387 -1.145 .472
19 4899 5083 350 498 4549 4585 5009 5205 438 586 4659 4707 0 0 2033 1613 1286 708 90 99 82 96 9134 9366 .992 1.008 1.01 1.136 .967 1.862 120 413 .961 .94 120 4750 7300 48 60 301 313 0 4935 483 4451 .979 5053 4570 1.022 .981 -.031 -.028
20 1569 1715 346 486 1223 1229 1600 1612 357 518 1254 1126 0 0 263 794 87 214 100 100 100 100 2452 2380 .995 1.005 .898 .919 .915 1.608 80 365 1.444 .72 110 4900 7290 47 58 316 327 0 1665 472 1193 .976 1565 1093 1.025 .872 -.036 -.198

Total number of rows: 43008

Table truncated, full table size 10145 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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