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Sample GSM184242 Query DataSets for GSM184242
Status Public on Aug 09, 2007
Title 251c1
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 251c1
Organism Helicobacter pylori
Characteristics 0.25 ug 251c1
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/2002-08/32396.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 6078 7601 555 451 5523 7150 4845 5372 557 458 4290 4921 0 0 4898 6419 89 88 87 86 85 81 12673 9211 .772 1.295 1.147 1.037 1.257 1.877 80 544 1.335 .97 100 1550 41460 65 75 90 100 0 9622 571 9051 1.639 6800 6229 .61 1.452 .713 .538
2 4121 1550 491 384 3630 1166 2932 843 498 388 2441 459 0 0 2941 2021 91 73 94 90 92 86 4796 2900 3.113 .321 .188 .207 .185 2.121 52 412 .403 .72 90 1810 41460 65 74 116 125 0 1962 486 1476 .407 1067 581 2.459 .238 -1.298 -2.071
3 7069 5838 469 372 6600 5466 6261 4497 480 384 5792 4125 0 0 5071 4603 99 109 100 92 94 92 12066 9917 1.207 .828 .712 .695 .713 1.565 52 412 .861 .97 90 2050 41460 65 74 140 149 0 7390 471 6919 1.048 5692 5222 .954 .902 .068 -.15
4 718 1111 457 332 261 779 563 481 456 348 106 149 0 0 513 1981 77 180 59 40 34 25 1040 255 .335 2.985 1.406 1.667 1.604 3.283 52 334 3.971 .71 80 2280 41470 67 75 164 172 0 1406 420 986 3.778 609 189 .265 1.779 1.918 .831
5 891 1217 450 329 441 888 553 458 454 336 103 129 0 0 937 2190 92 70 51 53 40 48 1329 232 .497 2.014 1.252 .861 .82 4.036 52 340 3.074 .7 80 2520 41480 68 76 188 196 0 1541 416 1124 2.549 580 163 .392 1.585 1.35 .665
6 11390 12329 472 377 10918 11952 7402 8917 476 389 6930 8540 0 0 9498 10136 102 88 100 100 100 100 22870 15470 .913 1.095 1.232 1.129 .99 1.991 52 340 1.086 .96 80 2760 41480 68 76 212 220 0 15606 477 15129 1.386 11287 10810 .722 1.56 .471 .641
7 899 1115 408 345 491 770 566 492 414 390 158 147 0 0 818 1467 83 575 59 34 50 26 1261 305 .638 1.568 .93 1.234 1.157 2.864 52 332 2.914 .72 80 3020 41470 67 75 238 246 0 1411 437 975 1.985 623 186 .504 1.178 .989 .236
8 940 1223 479 363 461 860 667 571 495 385 188 208 0 0 636 1675 116 111 61 53 46 48 1321 396 .536 1.866 1.106 1.031 1.183 3.749 52 332 2.498 .73 80 3260 41480 68 76 262 270 0 1548 459 1089 2.361 723 263 .423 1.4 1.24 .486
9 3730 4023 495 361 3235 3662 2417 2513 499 359 1922 2152 0 0 2941 3819 85 62 100 100 100 98 6897 4074 .883 1.132 1.12 1.014 1.054 1.657 52 332 1.24 .94 80 3500 41480 68 76 286 294 0 5092 457 4635 1.433 3181 2724 .698 1.417 .519 .503
10 954 1157 488 350 466 807 640 693 498 355 152 343 0 0 759 1236 85 67 60 71 48 63 1273 495 .577 1.732 2.257 1.486 1.4 3.145 80 552 1.787 .84 100 3720 41480 67 77 307 317 0 1465 443 1022 2.192 877 434 .456 2.856 1.132 1.514
11 826 1029 468 340 358 689 586 508 467 346 118 168 0 0 600 1767 88 65 55 72 38 52 1047 286 .52 1.925 1.424 1.413 1.371 2.879 80 552 3.249 .79 100 3960 41490 68 78 331 341 0 1303 430 872 2.436 643 213 .41 1.802 1.285 .85
12 7741 2049 531 372 7210 1677 7380 1190 535 380 6849 818 0 0 5205 3465 93 68 100 94 100 88 8887 7667 4.299 .233 .119 .127 .106 2.643 52 340 .199 .35 80 4220 41500 70 78 358 366 0 2594 471 2123 .294 1506 1035 3.396 .151 -1.764 -2.726
13 1966 2458 509 370 1457 2088 1341 1768 514 373 832 1398 0 0 1646 1977 86 73 90 98 80 92 3545 2230 .698 1.433 1.68 1.535 1.423 2.215 52 340 1.388 .77 80 4460 41500 70 78 382 390 0 3111 468 2643 1.814 2238 1770 .551 2.127 .859 1.089
14 8304 10310 519 398 7785 9912 8028 7752 526 412 7509 7354 0 0 5973 8285 100 90 100 98 100 96 17697 14863 .785 1.273 .979 1.125 1.207 1.972 52 337 1.347 .94 80 4700 41500 70 78 406 414 0 13051 504 12547 1.612 9813 9309 .62 1.24 .689 .31
15 1739 1903 481 333 1258 1570 929 653 492 342 448 320 0 0 1641 3705 88 74 73 71 61 65 2828 768 .801 1.248 .714 .783 .62 3.216 52 420 2.465 .72 90 4940 41500 69 78 429 438 0 2409 422 1987 1.58 827 405 .633 .904 .66 -.145
16 1544 2253 483 329 1061 1924 597 463 492 335 114 134 0 0 2106 4141 108 70 51 65 42 50 2985 248 .551 1.813 1.175 1.361 1.389 2.3 52 420 2.22 .8 90 5180 41500 69 78 453 462 0 2852 416 2435 2.295 586 170 .436 1.488 1.199 .573
17 2114 2519 463 324 1651 2195 1059 1060 465 331 596 736 0 0 2099 3387 81 57 96 98 86 94 3846 1332 .752 1.329 1.235 1.087 1.059 2.082 52 412 1.645 .84 90 5420 41500 69 78 477 486 0 3189 410 2778 1.683 1342 932 .594 1.563 .751 .644
18 3010 2689 529 488 2481 2201 1590 1216 535 503 1061 728 0 0 3043 3028 90 206 88 80 86 69 4682 1789 1.127 .887 .686 .684 .713 1.883 52 420 .956 .9 90 1570 41710 90 99 92 101 0 3404 618 2786 1.123 1539 922 .89 .869 .167 -.203
19 4862 4782 500 415 4362 4367 4761 4165 508 428 4261 3750 0 0 1802 2133 94 156 100 100 100 100 8729 8011 .999 1.001 .88 .973 .978 1.268 120 890 1.034 .96 130 1810 41670 84 97 114 127 0 6053 525 5528 1.267 5272 4747 .789 1.114 .342 .156
20 774 586 496 367 278 219 653 499 507 379 157 132 0 0 289 306 91 110 68 52 46 36 497 289 1.269 .788 .841 .702 .714 2.834 80 560 .989 .61 100 2050 41700 89 99 140 150 0 742 465 277 .997 632 167 1.003 1.064 -.004 .09

Total number of rows: 4608

Table truncated, full table size 1108 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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