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Sample GSM184253 Query DataSets for GSM184253
Status Public on Aug 09, 2007
Title 251f1 vs Tigr/Astra ref
Sample type genomic
 
Channel 1
Source name 0.25 ug Tigr/Astra genomic DNA reference
Organism Helicobacter pylori
Characteristics 0.25 ug Tigr/Astra genomic DNA reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.25 ug 251f1 genomic DNA
Organism Helicobacter pylori
Characteristics 0.25 ug 251f1 genomic DNA
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/2002-07/30943.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 4305 4193 326 298 3979 3895 3519 3433 419 322 3193 3135 0 0 3117 2913 1070 228 83 91 80 90 7874 6328 1.022 .979 .982 1.064 .988 1.35 80 648 .954 .99 110 2250 12110 95 106 99 110 0 5824 414 5410 1.36 4768 4354 .736 1.364 .443 .447
2 2924 529 375 336 2549 193 2272 417 393 338 1897 81 0 0 2735 319 365 72 90 56 73 28 2742 1978 13.207 .076 .043 .072 .078 2.477 80 643 .086 .83 110 2490 12110 95 106 123 134 0 735 467 268 .105 579 113 9.509 .059 -3.249 -4.076
3 7895 4875 417 380 7478 4495 5273 3207 454 397 4856 2827 0 0 6548 3861 318 181 98 98 98 98 11973 7683 1.664 .601 .582 .609 .595 1.131 80 656 .594 1 110 2730 12110 95 106 147 158 0 6771 528 6243 .835 4454 3926 1.198 .809 -.26 -.307
4 589 500 374 338 215 162 416 336 377 345 42 -2 0 0 401 314 67 61 40 34 32 32 377 40 1.327 .753 null .894 .89 2.406 52 420 .762 .9 90 2980 12110 96 105 173 182 0 694 469 225 1.047 467 null .956 null .066 null
5 531 490 377 347 154 143 313 300 379 351 -64 -47 0 0 409 338 64 59 34 36 30 36 297 -111 1.077 .929 null .948 .927 1.764 52 420 .817 .89 90 3220 12110 96 105 197 206 0 681 482 199 1.29 417 null .775 null .367 null
6 5024 3935 396 373 4628 3562 2739 2193 403 380 2343 1820 0 0 4754 3701 68 62 100 100 100 100 8190 4163 1.299 .77 .777 .732 .749 1.199 52 420 .768 .99 90 3460 12110 96 105 221 230 0 5465 518 4947 1.069 3046 2528 .935 1.079 .096 .11
7 1218 1028 362 356 856 672 856 755 374 360 494 399 0 0 804 628 82 73 93 93 86 78 1528 893 1.274 .785 .808 .756 .772 1.564 80 552 .775 .97 100 3700 12100 95 105 245 255 0 1428 494 933 1.09 1049 554 .917 1.122 .125 .166
8 548 432 334 317 214 115 417 351 337 320 83 34 0 0 280 197 53 50 58 43 47 37 329 117 1.861 .537 .41 .603 .636 2.603 80 560 .634 .84 100 3940 12110 96 106 269 279 0 600 440 160 .746 488 47 1.34 .569 -.422 -.814
9 3458 2439 340 319 3118 2120 2529 1968 346 322 2189 1649 0 0 2660 1692 67 59 99 98 95 96 5238 3838 1.471 .68 .753 .713 .688 1.339 120 870 .654 .99 130 4180 12080 91 104 291 304 0 3388 443 2944 .944 2733 2290 1.059 1.046 -.083 .065
10 656 628 363 337 293 291 506 513 366 337 143 176 0 0 406 327 65 57 63 71 52 57 584 319 1.007 .993 1.231 1.1 1.039 2.101 80 560 .855 .92 100 4420 12110 96 106 317 327 0 872 468 404 1.379 713 244 .725 1.709 .464 .773
11 673 650 418 389 255 261 472 482 424 395 54 93 0 0 449 423 88 82 47 50 42 42 516 147 .977 1.024 1.722 1.026 .934 2.592 80 560 .957 .95 100 4660 12110 96 106 341 351 0 903 540 363 1.422 669 129 .703 2.392 .507 1.258
12 4305 645 535 498 3770 147 2676 530 534 500 2141 32 0 0 3854 298 102 92 96 45 95 27 3917 2173 25.646 .039 .015 .057 .053 2.215 80 560 .055 .78 100 4890 12110 96 106 364 374 0 896 692 204 .054 736 44 18.465 .021 -4.207 -5.59
13 2545 2078 600 572 1945 1506 2181 1807 602 577 1581 1235 0 0 1279 957 114 106 96 96 96 96 3451 2816 1.292 .774 .781 .799 .781 1.288 156 1041 .753 .98 140 5130 12080 91 105 386 400 0 2886 794 2092 1.075 2510 1715 .93 1.085 .105 .118
14 5548 4714 711 676 4837 4038 4257 3854 734 701 3546 3178 0 0 4229 3537 156 138 98 100 95 95 8875 6724 1.198 .835 .896 .88 .879 1.293 80 560 .832 .99 100 5380 12110 96 106 413 423 0 6547 939 5608 1.159 5353 4414 .862 1.245 .213 .316
15 2615 1905 745 732 1870 1173 2713 1954 770 754 1968 1222 0 0 1197 841 152 150 88 84 86 82 3043 3190 1.594 .627 .621 .666 .638 1.949 52 320 .67 .97 80 5620 12090 95 103 438 446 0 2646 1017 1629 .871 2714 1697 1.148 .862 -.199 -.214
16 1932 1866 735 756 1197 1110 1465 1357 748 763 730 601 0 0 1450 1328 128 98 65 71 62 68 2307 1331 1.078 .927 .823 .903 .971 1.982 32 170 .924 .98 60 5860 12100 97 103 463 469 0 2592 1050 1542 1.288 1885 835 .776 1.143 .365 .193
17 2554 2414 732 735 1822 1679 1944 1962 736 736 1212 1227 0 0 1642 1447 95 93 90 93 87 87 3501 2439 1.085 .922 1.012 .965 .919 1.414 32 236 .896 .98 70 6100 12110 97 104 486 493 0 3353 1021 2332 1.28 2725 1704 .781 1.406 .356 .492
18 2706 1564 459 391 2247 1173 2393 1350 858 396 1934 959 0 0 1868 1010 3343 84 25 84 0 81 3420 2893 1.916 .522 .496 .495 .525 1.331 32 176 .536 .99 60 2270 12360 123 129 104 110 0 2172 543 1629 .725 1875 1332 1.379 .689 -.464 -.538
19 4012 2703 453 410 3559 2293 2813 1796 460 411 2360 1386 0 0 2987 2207 102 86 100 98 100 95 5852 3746 1.552 .644 .587 .57 .604 1.315 120 907 .688 .99 130 2510 12330 116 129 124 137 0 3754 569 3185 .895 2494 1925 1.118 .816 -.16 -.294
20 1242 1015 471 423 771 592 1400 1132 469 418 929 709 0 0 787 544 130 113 67 69 65 67 1363 1638 1.302 .768 .763 .778 .783 1.46 52 340 .71 .97 80 2800 12330 119 127 156 164 0 1410 588 822 1.066 1572 985 .938 1.06 .093 .084

Total number of rows: 4608

Table truncated, full table size 1094 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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