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Sample GSM69949 Query DataSets for GSM69949
Status Public on Aug 16, 2005
Title J99-D1-3 vs Tigr/Astra references (250 ug).
Sample type genomic
 
Channel 1
Source name 250 ng Tigr/Astra genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng Tigr/Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 250 ng J99-D1 genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng J99-D1 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18853.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 15, 2005
Last update date Sep 22, 2006
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 GPL15
Series (1)
GSE3137 H. pilory diversity in human

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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

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 VALUE LOG_RAT2N_MEDIAN
1 18749 14242 1391 385 17358 13857 18979 14671 1409 400 17588 14286 0 0 1960 2051 254 129 100 100 100 100 31215 31874 1.253 .798 .812 .793 .815 1.112 52 420 .807 .99 90 1090 41270 58 67 36 45 0 19852 537 19316 1.113 20450 19914 .899 1.132 .154 .179
2 9752 812 1430 366 8322 446 10139 801 1451 374 8709 435 0 0 2364 218 268 101 100 98 100 86 8768 9144 18.659 .054 .05 .05 .049 1.556 52 420 .053 .83 90 1330 41270 58 67 60 69 0 1132 510 622 .075 1117 606 13.386 .07 -3.743 -3.844
3 13138 10094 1400 387 11738 9707 13407 10214 1866 563 12007 9827 0 0 1923 1311 3976 1457 100 100 94 100 21445 21834 1.209 .827 .818 .832 .819 1.124 52 420 .813 .97 90 1550 41250 56 65 82 91 0 14070 539 13531 1.153 14238 13698 .867 1.141 .205 .19
4 2517 598 1355 363 1162 235 1523 460 1349 364 168 97 0 0 6367 553 229 100 41 50 26 31 1397 265 4.945 .202 .577 .341 .301 2.827 80 656 .083 .86 110 1790 41250 55 66 105 116 -100 834 506 328 .282 641 135 3.547 .805 -1.827 -.313
5 1758 451 1413 368 345 83 1620 413 1436 381 207 45 0 0 583 165 275 106 41 30 25 18 428 252 4.157 .241 .217 .325 .327 3.294 80 642 .152 .42 110 2030 41250 55 66 129 140 -100 629 513 116 .335 576 63 2.982 .303 -1.576 -1.722
6 8638 2843 1401 402 7237 2441 8663 2903 1428 412 7262 2501 0 0 1623 637 335 115 100 100 100 100 9678 9763 2.965 .337 .344 .333 .337 1.232 208 1382 .33 .97 170 2270 41250 52 69 150 167 0 3963 560 3403 .47 4047 3486 2.127 .48 -1.089 -1.059
7 2317 978 1367 410 950 568 1693 591 1386 419 326 181 0 0 1404 799 287 112 53 58 32 46 1518 507 1.673 .598 .555 .482 .515 3.097 80 634 .518 .87 110 2510 41240 54 65 177 188 -100 1363 572 792 .833 824 252 1.2 .774 -.263 -.37
8 2070 721 1376 398 694 323 1632 514 1399 413 256 116 0 0 991 518 265 117 48 50 36 35 1017 372 2.149 .465 .453 .391 .476 2.884 80 648 .419 .77 110 2750 41240 54 65 201 212 -100 1005 555 450 .649 716 162 1.541 .632 -.624 -.663
9 11425 8869 1575 437 9850 8432 12225 9042 1600 453 10650 8605 0 0 2943 2297 434 150 100 100 100 100 18282 19255 1.168 .856 .808 .867 .863 1.204 52 415 .831 .98 90 2990 41240 55 64 226 235 0 12363 609 11754 1.193 12604 11995 .838 1.126 .255 .172
10 1741 671 1450 420 291 251 1539 544 1474 430 89 124 0 0 682 387 272 117 35 52 20 31 542 213 1.159 .863 1.393 .646 .669 3.37 80 656 .427 .66 110 3240 41240 54 65 250 261 -100 935 585 350 1.202 758 173 .832 1.942 .266 .958
11 2191 881 1473 422 718 459 1794 615 1484 431 321 193 0 0 959 567 253 108 55 65 33 45 1177 514 1.564 .639 .601 .706 .628 2.438 80 656 .525 .8 110 3480 41240 54 65 274 285 -100 1228 588 640 .891 857 269 1.122 .838 -.166 -.255
12 7019 615 1499 449 5520 166 7069 601 1518 466 5570 152 0 0 862 147 288 142 100 50 100 19 5686 5722 33.253 .03 .027 .036 .035 1.707 52 412 .022 .33 90 3720 41230 54 63 299 308 0 857 626 231 .042 838 212 23.856 .038 -4.576 -4.716
13 4663 5410 1614 455 3049 4955 4664 5167 1638 513 3050 4712 0 0 927 1040 357 342 100 100 96 100 8004 7762 .615 1.625 1.545 1.699 1.526 1.501 32 236 1.52 .92 70 3950 41240 56 63 323 330 0 7541 634 6907 2.265 7202 6568 .441 2.154 1.18 1.107
14 6455 3549 1535 444 4920 3105 6700 3704 1566 454 5165 3260 0 0 2015 1261 262 113 100 100 100 100 8025 8425 1.585 .631 .631 .633 .646 1.223 52 340 .622 .96 80 4210 41240 56 64 349 357 0 4947 619 4328 .88 5163 4544 1.137 .88 -.185 -.185
15 3218 590 1446 447 1772 143 1844 471 1468 461 398 24 0 0 2505 315 259 122 60 36 46 28 1915 422 12.392 .081 .06 .184 .129 3.56 80 648 .092 .66 110 4440 41230 53 64 370 381 -100 822 623 199 .112 657 33 8.89 .084 -3.152 -3.573
16 2618 1099 1385 449 1233 650 1893 672 1401 461 508 223 0 0 1958 1029 250 118 67 65 51 48 1883 731 1.897 .527 .439 .503 .521 2.639 80 648 .483 .88 110 4680 41230 53 64 394 405 -100 1532 626 906 .735 937 311 1.361 .612 -.445 -.709
17 3157 2091 1501 461 1656 1630 2508 1697 1522 472 1007 1236 0 0 1997 1730 295 130 81 90 70 85 3286 2243 1.016 .984 1.227 1.027 1 1.828 80 648 .885 .91 110 4920 41230 53 64 418 429 -100 2915 643 2272 1.372 2365 1723 .729 1.711 .456 .775
18 2853 993 1339 355 1514 638 1717 504 1383 368 378 149 0 0 2557 1248 795 111 32 58 25 41 2152 527 2.373 .421 .394 .397 .359 2.429 80 648 .459 .95 110 1070 41490 79 90 33 44 -100 1384 495 889 .587 703 208 1.702 .549 -.768 -.864
19 5801 3256 1411 372 4390 2884 5861 3080 1437 376 4450 2708 0 0 2354 1488 275 99 100 100 100 100 7274 7158 1.522 .657 .609 .668 .639 1.263 32 236 .652 .96 70 1320 41480 80 87 60 67 0 4539 519 4020 .916 4293 3775 1.092 .848 -.127 -.237
20 1619 494 1419 387 200 107 1379 383 2082 640 -40 -4 0 0 754 350 4614 1748 0 0 0 0 307 -44 1.869 .535 null .55 .512 3.797 80 599 .334 .7 110 1550 41490 79 90 81 92 -100 689 539 149 .746 534 -6 1.341 null -.423 null

Total number of rows: 4608

Table truncated, full table size 1121 Kbytes.




Supplementary data files not provided
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