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Sample GSM90756 Query DataSets for GSM90756
Status Public on Jan 06, 2006
Title HUMAN 1 [HSR (human female) vs. HSR (human 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 Human female genomic DNA
Organism Homo sapiens
Characteristics Human female genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35264.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 1255 925 383 438 872 487 1187 878 389 451 804 440 0 0 450 288 95 129 98 92 98 76 1359 1244 1.791 .558 .547 .568 .56 1.907 52 256 .528 .77 80 2420 7780 78 86 78 86 0 1076 509 566 .649 1021 512 1.54 .636 -.623 -.652
2 2079 1706 382 463 1697 1243 1957 1707 392 467 1575 1244 0 0 647 626 103 128 100 100 100 96 2940 2819 1.365 .732 .79 .675 .718 1.498 52 310 .738 .89 90 2560 7780 77 86 91 100 0 1984 538 1445 .852 1985 1447 1.174 .918 -.232 -.123
3 2659 1402 426 523 2233 879 2734 1412 421 515 2308 889 0 0 489 509 111 130 100 100 100 91 3112 3197 2.54 .394 .385 .327 .362 1.771 12 62 .455 .84 40 2710 7770 79 83 109 113 0 1630 608 1022 .458 1642 1034 2.185 .448 -1.127 -1.159
4 1784 1015 384 465 1400 550 1902 1027 386 463 1518 562 0 0 681 416 94 140 93 81 93 71 1950 2080 2.545 .393 .37 .405 .426 1.9 32 170 .442 .75 60 2850 7770 78 84 122 128 0 1180 541 640 .457 1194 653 2.189 .43 -1.13 -1.216
5 3776 2607 391 451 3385 2156 3718 2658 393 455 3327 2207 0 0 1229 802 98 126 100 100 100 100 5541 5534 1.57 .637 .663 .634 .65 1.552 52 336 .622 .92 90 3000 7770 76 85 135 144 0 3031 524 2507 .741 3091 2566 1.35 .771 -.433 -.375
6 1925 1357 396 457 1529 900 1923 1294 400 463 1527 837 0 0 647 526 106 151 100 92 98 86 2429 2364 1.699 .589 .548 .564 .559 1.82 52 255 .606 .87 80 3150 7780 78 86 151 159 0 1578 531 1047 .684 1505 973 1.461 .637 -.547 -.65
7 3118 1942 381 446 2737 1496 3137 1951 395 469 2756 1505 0 0 594 456 117 213 100 100 100 100 4233 4261 1.83 .547 .546 .536 .532 1.324 32 207 .522 .85 70 3290 7770 77 84 165 172 0 2258 519 1740 .636 2269 1750 1.573 .635 -.654 -.655
8 2264 1803 378 453 1886 1350 2201 1771 381 458 1823 1318 0 0 828 806 102 119 100 96 100 92 3236 3141 1.397 .716 .723 .64 .774 1.804 52 248 .76 .91 80 3430 7770 77 85 179 187 0 2097 527 1570 .832 2059 1533 1.201 .841 -.265 -.25
9 2506 1784 383 457 2123 1327 2452 1689 389 468 2069 1232 0 0 829 616 106 127 100 100 100 98 3450 3301 1.6 .625 .595 .603 .597 1.34 80 405 .622 .93 100 3580 7770 76 86 193 203 0 2074 531 1543 .727 1964 1433 1.376 .692 -.46 -.53
10 1559 1274 426 487 1133 787 1576 1264 440 502 1150 777 0 0 330 283 137 130 100 100 100 100 1920 1927 1.44 .695 .676 .679 .571 1.509 12 104 .591 .72 50 3730 7780 79 84 210 215 0 1481 566 915 .808 1470 903 1.238 .786 -.308 -.348
11 2388 1682 384 490 2004 1192 2267 1634 398 507 1883 1144 0 0 592 451 152 179 100 98 100 98 3196 3027 1.681 .595 .608 .564 .585 1.533 52 331 .621 .89 90 3870 7760 75 84 222 231 0 1956 570 1386 .692 1900 1330 1.446 .706 -.532 -.501
12 2853 2206 381 468 2472 1738 2096 1680 385 477 1715 1212 0 0 1708 1277 102 135 100 100 100 97 4210 2927 1.422 .703 .707 .667 .713 1.728 80 351 .683 .86 100 4020 7770 76 86 237 247 0 2565 544 2021 .818 1953 1409 1.223 .822 -.291 -.283
13 2436 1873 356 435 2080 1438 2355 1803 366 440 1999 1368 0 0 740 653 109 128 100 100 100 100 3518 3367 1.446 .691 .684 .659 .656 1.407 80 350 .708 .92 110 4160 7770 75 86 250 261 0 2178 506 1672 .804 2097 1591 1.244 .796 -.315 -.33
14 2877 1931 355 413 2522 1518 2881 1947 364 418 2526 1534 0 0 823 605 104 123 99 95 98 93 4040 4060 1.661 .602 .607 .572 .614 1.836 120 508 .621 .94 130 4300 7770 74 87 263 276 0 2245 480 1765 .7 2264 1784 1.429 .706 -.515 -.502
15 2358 1533 359 421 1999 1112 2349 1496 366 437 1990 1075 0 0 374 314 97 130 100 100 100 100 3111 3065 1.798 .556 .54 .542 .586 1.398 80 348 .526 .88 110 4460 7770 75 86 280 291 0 1783 490 1293 .647 1740 1250 1.546 .628 -.629 -.671
16 8150 6348 364 446 7786 5902 8426 6601 371 458 8062 6155 0 0 2216 2062 98 159 100 98 100 98 13688 14217 1.319 .758 .763 .713 .757 1.511 120 528 .774 .97 130 4590 7770 74 87 292 305 0 7381 519 6863 .881 7676 7157 1.135 .888 -.182 -.172
17 3459 2778 363 408 3096 2370 3167 2553 371 420 2804 2145 0 0 1459 961 99 151 98 100 98 100 5466 4949 1.306 .766 .765 .787 .759 1.384 120 441 .735 .95 120 4750 7780 76 88 309 321 0 3230 474 2756 .89 2969 2494 1.123 .89 -.168 -.169
18 624 625 363 415 261 210 407 544 374 423 44 129 0 0 464 349 98 117 36 51 26 26 471 173 1.243 .805 2.932 1.107 1.111 4.693 52 191 .737 .68 80 4900 7770 77 85 326 334 -50 727 483 244 .936 633 150 1.069 3.409 -.096 1.769
19 10459 8774 364 436 10095 8338 9769 8876 378 448 9405 8440 0 0 5685 4318 104 126 98 100 98 100 18433 17845 1.211 .826 .897 .925 .843 1.822 120 410 .799 .96 120 5040 7780 76 88 338 350 0 10202 507 9695 .96 10321 9814 1.041 1.043 -.058 .061
20 3499 2564 353 436 3146 2128 3566 2501 367 444 3213 2065 0 0 833 585 101 132 100 100 100 100 5274 5278 1.478 .676 .643 .678 .684 1.255 80 348 .678 .94 110 5180 7770 75 86 352 363 0 2981 507 2474 .787 2908 2401 1.271 .747 -.346 -.42

Total number of rows: 43008

Table truncated, full table size 10081 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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