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Sample GSM184284 Query DataSets for GSM184284
Status Public on Aug 09, 2007
Title 249i7
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 249i7
Organism Helicobacter pylori
Characteristics 0.25 ug 249i7
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/2002-08/32371.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 2932 4097 387 424 2545 3673 2139 2784 385 443 1752 2360 0 0 1877 2860 60 96 100 100 100 100 6218 4112 .693 1.443 1.347 1.333 1.439 1.507 52 340 1.501 .96 80 1850 41320 88 96 137 145 0 3725 385 3339 1.312 2531 2145 .762 1.225 .392 .292
2 3140 900 378 421 2762 479 3255 711 412 442 2877 290 0 0 1439 531 180 109 100 83 100 58 3241 3167 5.766 .173 .101 .136 .155 2.064 12 98 .302 .42 50 2080 41310 88 93 161 166 0 818 383 435 .158 646 264 6.343 .092 -2.665 -3.448
3 3395 3100 403 461 2992 2639 2883 2761 478 624 2480 2300 0 0 1921 1686 577 1160 100 68 84 46 5631 4780 1.134 .882 .927 .854 .887 1.467 32 176 .879 .96 60 2330 41320 89 95 186 192 0 2818 419 2399 .802 2510 2091 1.247 .843 -.319 -.246
4 427 598 385 467 42 131 372 483 412 506 -13 16 0 0 200 556 394 523 5 5 1 3 173 3 .321 3.119 null 1.334 1.39 4.134 80 560 3.314 .69 100 2570 41320 87 97 208 218 0 544 425 119 2.835 439 15 .353 null 1.504 null
5 691 1115 436 539 255 576 487 556 542 862 51 17 0 0 1404 3005 944 2783 5 3 1 2 831 68 .443 2.259 .333 1.338 .957 3.792 80 560 3.093 .92 100 2820 41320 87 97 233 243 0 1014 490 524 2.053 505 15 .487 .303 1.038 -1.722
6 2172 1667 394 436 1778 1231 950 835 395 452 556 399 0 0 3050 2119 64 151 82 66 70 52 3009 955 1.444 .692 .718 .705 .693 2.328 80 552 .677 .93 100 3070 41310 86 96 258 268 0 1515 396 1119 .629 759 363 1.589 .652 -.668 -.616
7 651 823 372 410 279 413 442 521 379 415 70 111 0 0 435 709 72 73 47 62 35 38 692 181 .676 1.48 1.586 1.409 1.281 3.725 80 560 1.892 .79 100 3290 41320 87 97 280 290 0 748 373 375 1.346 474 101 .743 1.442 .428 .528
8 438 543 353 391 85 152 387 417 359 402 34 26 0 0 184 487 122 100 17 21 10 12 237 60 .559 1.788 .765 1.329 1.367 3.624 80 560 2.032 .58 100 3530 41320 87 97 304 314 0 494 355 138 1.626 379 24 .615 .695 .701 -.525
9 1659 2330 370 392 1289 1938 1539 1765 370 403 1169 1373 0 0 972 1635 59 87 96 100 93 93 3227 2542 .665 1.503 1.175 1.483 1.482 1.99 32 170 1.618 .95 60 3790 41310 88 94 332 338 0 2118 356 1762 1.367 1605 1248 .732 1.068 .451 .095
10 509 712 346 384 163 328 393 464 348 387 47 80 0 0 296 595 60 61 45 51 31 42 491 127 .497 2.012 1.702 1.551 1.556 2.193 80 552 2.128 .87 100 4030 41310 86 96 354 364 0 647 349 298 1.829 422 73 .547 1.547 .871 .63
11 457 585 331 377 126 208 375 425 334 380 44 48 0 0 268 465 57 57 40 42 28 33 334 92 .606 1.651 1.091 1.312 1.299 3.295 80 560 1.808 .86 100 4250 41320 87 97 376 386 0 532 343 189 1.501 386 44 .666 .992 .586 -.012
12 3598 940 353 392 3245 548 3540 876 387 398 3187 484 0 0 1589 435 182 72 100 90 100 84 3793 3671 5.922 .169 .152 .139 .158 1.806 32 230 .201 .73 70 4500 41310 87 94 402 409 0 855 356 498 .154 796 440 6.514 .138 -2.703 -2.857
13 1747 2293 372 421 1375 1872 1359 1761 530 602 987 1340 0 0 1120 1533 572 687 71 71 45 50 3247 2327 .735 1.361 1.358 1.357 1.349 1.648 80 552 1.326 .94 100 4740 41310 86 96 425 435 0 2085 383 1702 1.238 1601 1218 .808 1.234 .308 .304
14 6752 9780 377 440 6375 9340 7196 10722 376 452 6819 10282 0 0 3372 5650 74 119 100 100 100 96 15715 17101 .683 1.465 1.508 1.241 1.386 1.504 32 148 1.561 .96 60 4970 41290 86 92 450 456 0 8891 400 8491 1.332 9747 9347 .751 1.371 .413 .455
15 894 1087 352 400 542 687 518 601 368 418 166 201 0 0 814 1043 221 113 43 52 35 47 1229 367 .789 1.268 1.211 1.033 1.105 2.576 80 522 1.341 .88 100 5210 41290 84 94 472 482 0 988 364 625 1.152 546 183 .868 1.101 .205 .139
16 584 704 336 376 248 328 410 457 340 383 74 81 0 0 532 755 60 69 51 53 36 38 576 155 .756 1.323 1.095 1.163 1.218 3.356 80 538 1.46 .88 100 5470 41300 85 95 498 508 0 640 342 298 1.202 415 74 .832 .995 .266 -.007
17 686 759 351 376 335 383 380 433 354 387 29 57 0 0 715 855 60 79 37 38 30 26 718 86 .875 1.143 1.966 1.101 1.207 3.378 80 516 1.221 .84 100 5710 41300 85 95 522 532 0 690 342 348 1.039 394 52 .962 1.787 .056 .837
18 5604 2678 387 419 5217 2259 5780 3247 406 442 5393 2828 0 0 724 1250 176 138 100 100 100 100 7476 8221 2.309 .433 .524 .337 .533 2.947 4 20 .552 .82 30 1860 41550 113 116 140 143 0 2435 381 2054 .394 2952 2571 2.54 .477 -1.345 -1.069
19 2328 2126 374 434 1954 1692 2122 1913 393 453 1748 1479 0 0 889 1012 106 107 100 100 100 96 3646 3227 1.155 .866 .846 .767 .833 1.539 52 340 .942 .94 80 2110 41530 109 117 163 171 0 1933 395 1538 .787 1739 1345 1.27 .769 -.345 -.379
20 493 565 402 459 91 106 422 442 406 470 20 -17 0 0 220 420 72 99 32 27 23 22 197 3 .858 1.165 null 1.172 1.097 2.979 80 560 2.134 .69 100 2360 41540 109 119 187 197 0 514 417 96 1.059 402 null .944 null .083 null

Total number of rows: 4608

Table truncated, full table size 1089 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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