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Sample GSM184261 Query DataSets for GSM184261
Status Public on Aug 09, 2007
Title 259c9 rep2
Sample type genomic
 
Channel 1
Source name 0.25 ug Tigr/Astra Reference
Organism Helicobacter pylori
Characteristics 0.25 ug Tigr/Astra Reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.25 ug 259c9
Organism Helicobacter pylori
Characteristics 0.25 ug 259c9
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: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32400.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 Apr 25, 2007
Last update date Aug 08, 2007
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)
GSE7618 Array CGH of Mexican Patient Isolates and BCS100 Strain

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 7171 7416 719 588 6452 6828 5203 5588 744 614 4484 5000 0 0 5168 5303 172 230 95 95 92 92 13280 9484 .945 1.058 1.115 1.092 1.053 1.549 80 560 1.041 1 100 1720 39870 89 99 96 106 0 8240 653 7587 1.176 6209 5556 .85 1.239 .234 .309
2 5498 1838 711 577 4787 1261 4820 1353 717 575 4109 776 0 0 3450 1235 101 123 94 84 94 80 6048 4885 3.796 .263 .189 .214 .187 2.676 52 412 .248 .77 90 1950 39860 88 97 119 128 0 2042 641 1401 .293 1503 862 3.417 .21 -1.773 -2.253
3 9946 8615 698 525 9248 8090 7547 6714 714 534 6849 6189 0 0 7321 6172 110 126 100 100 100 100 17338 13038 1.143 .875 .904 .885 .871 1.178 52 332 .863 1 80 2210 39860 89 97 146 154 0 9572 583 8989 .972 7460 6877 1.029 1.004 -.041 .006
4 1021 1080 684 469 337 611 752 551 690 481 68 82 0 0 684 1276 98 114 40 46 27 30 948 150 .552 1.813 1.206 1.403 1.769 2.656 80 560 1.866 .96 100 2440 39870 89 99 168 178 0 1200 521 679 2.015 612 91 .496 1.34 1.01 .422
5 981 1093 721 553 260 540 743 632 731 573 22 79 0 0 605 1017 111 129 37 42 27 35 800 101 .481 2.077 3.591 1.273 1.592 3.174 80 560 1.741 .93 100 2680 39870 89 99 192 202 0 1214 614 600 2.308 702 88 .433 3.99 1.206 1.996
6 13780 6048 726 583 13054 5465 10899 5477 747 594 10173 4894 0 0 9880 4229 147 141 100 98 100 96 18519 15067 2.389 .419 .481 .382 .37 1.51 52 420 .417 .98 90 2920 39870 89 98 216 225 0 6720 648 6072 .465 6086 5438 2.15 .535 -1.104 -.904
7 1495 1984 707 600 788 1384 892 951 715 609 185 351 0 0 1107 2019 101 107 55 55 48 51 2172 536 .569 1.756 1.897 1.612 1.822 2.494 52 340 1.813 .98 80 3140 39870 90 98 239 247 0 2204 667 1538 1.951 1057 390 .512 2.108 .965 1.076
8 1212 1363 684 564 528 799 774 533 692 565 90 -31 0 0 856 1492 89 97 50 36 36 34 1327 59 .661 1.513 null 1.545 1.624 2.952 52 340 1.741 .95 80 3380 39870 90 98 263 271 0 1514 627 888 1.681 592 null .595 null .75 null
9 2042 1946 748 590 1294 1356 1343 1157 1026 880 595 567 0 0 1804 2069 2188 1976 15 21 11 13 2650 1162 .954 1.048 .953 .921 .972 1.946 52 340 1.094 .99 80 3620 39870 90 98 287 295 0 2162 656 1507 1.164 1286 630 .859 1.059 .22 .082
10 1246 1601 701 549 545 1052 917 1114 705 552 216 565 0 0 789 1342 100 97 57 69 50 59 1597 781 .518 1.93 2.616 1.682 1.808 2.57 52 340 1.853 .95 80 3860 39870 90 98 311 319 0 1779 610 1169 2.145 1238 628 .466 2.906 1.101 1.539
11 1096 1176 698 529 398 647 827 699 703 532 129 170 0 0 662 1101 95 91 53 55 46 48 1045 299 .615 1.626 1.318 1.295 1.645 2.801 52 340 1.543 .95 80 4100 39870 90 98 335 343 0 1307 588 719 1.806 777 189 .554 1.464 .853 .55
12 6244 5069 761 570 5483 4499 5596 5052 841 627 4835 4482 0 0 4749 3736 612 300 86 88 76 78 9982 9317 1.219 .821 .927 .725 .778 1.768 52 340 .814 .97 80 4340 39870 90 98 359 367 0 5632 633 4999 .912 5613 4980 1.097 1.03 -.133 .043
13 1906 2383 763 540 1143 1843 1335 1569 777 570 572 1029 0 0 1177 1789 151 165 75 84 73 73 2986 1601 .62 1.612 1.799 1.559 1.563 1.611 52 340 1.564 .98 80 4580 39870 90 98 383 391 0 2648 600 2048 1.792 1743 1143 .558 1.999 .841 .999
14 6920 8488 774 599 6146 7889 6214 8197 801 660 5440 7598 0 0 4469 5474 240 437 100 100 90 88 14035 13038 .779 1.284 1.397 1.368 1.297 1.224 52 340 1.257 .99 80 4820 39870 90 98 407 415 0 9431 666 8766 1.426 9108 8442 .701 1.552 .512 .634
15 1908 1547 723 506 1185 1041 1109 906 745 528 386 400 0 0 1484 1336 236 243 57 51 48 50 2226 786 1.138 .878 1.036 .818 .85 2.624 52 340 .9 .95 80 5060 39870 90 98 431 439 0 1719 562 1157 .976 1007 444 1.024 1.151 -.035 .203
16 1461 1447 704 486 757 961 938 656 716 501 234 170 0 0 1085 1522 98 106 65 55 51 48 1718 404 .788 1.269 .726 1.052 1.2 2.354 52 340 1.403 .93 80 5300 39870 90 98 455 463 0 1608 540 1068 1.411 729 189 .709 .807 .496 -.309
17 1646 1986 705 519 941 1467 1124 1084 710 528 419 565 0 0 1201 1889 100 114 78 80 69 73 2408 984 .641 1.559 1.348 1.291 1.514 1.981 52 340 1.503 .96 80 5540 39870 90 98 479 487 0 2207 577 1630 1.732 1204 628 .577 1.498 .793 .583
18 3476 2532 726 482 2750 2050 2174 1837 754 518 1448 1355 0 0 3246 2240 156 148 94 82 86 73 4800 2803 1.341 .745 .936 .643 .695 1.919 52 340 .704 .98 80 1730 40100 113 121 98 106 0 2813 536 2278 .828 2041 1506 1.207 1.04 -.272 .056
19 4854 4586 719 478 4135 4108 4682 4641 741 504 3963 4163 0 0 1664 1684 158 144 100 100 100 100 8243 8126 1.007 .993 1.05 .987 .977 1.189 80 560 .981 .99 100 1950 40080 110 120 119 129 0 5096 531 4564 1.104 5157 4626 .906 1.167 .143 .223
20 1672 1877 711 505 961 1372 1627 1604 741 565 916 1099 0 0 673 1175 195 284 84 78 75 78 2333 2015 .7 1.428 1.2 1.251 1.238 2.014 52 340 1.809 .94 80 2200 40100 113 121 145 153 0 2086 561 1524 1.586 1782 1221 .63 1.333 .666 .415

Total number of rows: 4608

Table truncated, full table size 1107 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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