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Sample GSM184223 Query DataSets for GSM184223
Status Public on Aug 09, 2007
Title 251i1 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 251i1
Organism Helicobacter pylori
Characteristics 0.25 ug 251i1
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/2002-08/32422.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 6903 10850 450 409 6453 10441 6494 9689 480 499 6044 9280 0 0 6555 10235 154 342 88 82 80 77 16894 15324 .618 1.618 1.535 1.692 1.592 1.395 80 502 1.584 1 100 1120 39820 106 116 53 63 0 10960 413 10546 1.634 9787 9374 .612 1.551 .709 .633
2 5668 927 429 378 5239 549 3258 750 438 384 2829 372 0 0 5522 564 79 85 98 84 96 75 5788 3201 9.543 .105 .131 .105 .106 1.621 52 340 .101 .97 80 1360 39820 107 115 78 86 0 936 382 555 .106 758 376 9.447 .133 -3.24 -2.912
3 7354 7248 429 391 6925 6857 6269 6367 433 402 5840 5976 0 0 5761 5504 85 93 92 94 92 92 13782 11816 1.01 .99 1.023 .999 1.006 1.358 52 340 .973 1 80 1600 39810 106 114 102 110 0 7321 395 6926 1 6431 6036 1 1.034 0 .048
4 585 495 416 379 169 116 505 462 424 383 89 83 0 0 238 178 73 79 55 51 32 26 285 172 1.457 .686 .933 .9 .923 3.819 52 412 .715 .53 90 1850 39800 104 113 126 135 0 500 383 117 .693 467 84 1.442 .942 -.528 -.086
5 596 495 456 424 140 71 505 459 461 430 49 35 0 0 233 173 87 91 44 30 32 19 211 84 1.972 .507 .714 .808 .753 3.279 52 412 .735 .55 90 2090 39800 104 113 150 159 0 500 428 72 .512 464 35 1.952 .722 -.965 -.471
6 10388 10335 483 464 9905 9871 10206 10553 487 474 9723 10089 0 0 6888 6917 96 107 100 100 100 100 19776 19812 1.003 .997 1.038 1.004 1.002 1.188 52 412 .998 1 90 2330 39800 104 113 174 183 0 10439 469 9971 1.007 10660 10191 .993 1.048 .01 .068
7 752 733 443 419 309 314 499 490 444 421 56 71 0 0 664 608 80 78 45 48 37 42 623 127 .984 1.016 1.268 .908 .952 3.153 80 552 .924 .94 100 2590 39800 104 114 200 210 0 740 423 317 1.026 495 72 .974 1.281 .038 .357
8 602 527 454 442 148 85 518 503 458 449 64 61 0 0 256 155 86 93 42 40 25 20 233 125 1.741 .574 .953 .921 .908 3.819 80 552 .529 .49 100 2830 39800 104 114 224 234 0 532 446 86 .58 508 62 1.724 .963 -.786 -.055
9 4958 5039 482 493 4476 4546 4867 4603 488 503 4385 4110 0 0 3391 3439 89 104 92 92 92 90 9022 8495 .985 1.016 .937 1.043 1.003 1.299 52 332 1.014 .99 80 3060 39800 105 113 248 256 0 5090 498 4592 1.026 4649 4152 .975 .947 .037 -.079
10 788 806 469 479 319 327 723 724 472 478 254 245 0 0 338 266 79 93 80 84 63 61 646 499 .976 1.025 .965 .915 .965 1.867 52 332 .896 .79 80 3300 39800 105 113 272 280 0 814 484 330 1.035 731 247 .966 .974 .05 -.038
11 684 752 449 481 235 271 568 645 458 485 119 164 0 0 316 355 81 91 61 51 46 46 506 283 .867 1.153 1.378 1.003 1.094 2.549 52 332 1.189 .81 80 3540 39800 105 113 296 304 0 760 486 274 1.165 652 166 .858 1.392 .22 .477
12 5686 1203 462 467 5224 736 4484 1110 462 475 4022 643 0 0 3346 728 84 87 100 92 100 80 5960 4665 7.098 .141 .16 .121 .108 2.128 52 332 .114 .67 80 3780 39800 105 113 320 328 0 1215 472 743 .142 1121 649 7.027 .161 -2.813 -2.631
13 1745 2335 445 464 1300 1871 1311 1571 447 472 866 1107 0 0 1319 1973 79 91 84 88 82 86 3171 1973 .695 1.439 1.278 1.463 1.433 1.907 52 412 1.477 .98 90 4000 39790 103 112 341 350 0 2359 469 1890 1.454 1587 1118 .688 1.291 .54 .369
14 5330 8061 431 458 4899 7603 4784 6660 434 457 4353 6202 0 0 3651 6010 80 93 98 96 96 94 12502 10555 .644 1.552 1.425 1.501 1.537 1.327 52 412 1.596 .99 90 4240 39790 103 112 365 374 0 8142 463 7680 1.568 6727 6265 .638 1.439 .649 .525
15 969 703 410 395 559 308 599 493 411 400 189 98 0 0 749 436 77 81 63 53 53 44 867 287 1.815 .551 .519 .774 .678 2.861 52 400 .548 .91 90 4480 39780 102 111 389 398 0 710 399 311 .557 498 99 1.797 .524 -.845 -.933
16 779 800 416 396 363 404 620 599 421 407 204 203 0 0 588 623 77 87 78 76 55 55 767 407 .899 1.113 .995 1.097 1.15 1.819 52 400 1.089 .94 90 4720 39780 102 111 413 422 0 808 400 408 1.124 605 205 .89 1.005 .169 .007
17 1024 1340 402 403 622 937 751 852 410 412 349 449 0 0 901 1420 93 132 71 76 63 63 1559 798 .664 1.506 1.287 1.281 1.481 2.135 52 400 1.354 .98 90 4960 39780 102 111 437 446 0 1354 407 946 1.522 861 454 .657 1.3 .606 .378
18 930 1515 519 479 411 1036 865 1606 612 831 346 1127 0 0 683 794 254 656 59 65 36 44 1447 1473 .397 2.521 3.257 2.309 2.826 2.481 52 400 2.335 .75 90 1140 40030 127 136 55 64 0 1530 484 1046 2.546 1622 1138 .393 3.29 1.348 1.718
19 4614 4295 489 451 4125 3844 3985 3502 494 465 3496 3051 0 0 1716 1964 94 105 100 100 100 100 7969 6547 1.073 .932 .873 .898 .919 1.145 52 420 .929 .98 90 1380 40030 127 136 79 88 0 4338 456 3883 .941 3537 3082 1.062 .882 -.087 -.182
20 719 563 481 446 238 117 548 479 494 467 67 33 0 0 356 256 127 154 44 30 38 21 355 100 2.034 .492 .493 .709 .598 3.421 52 420 .747 .81 90 1620 40030 127 136 103 112 0 569 451 118 .497 484 33 2.014 .498 -1.01 -1.007

Total number of rows: 4608

Table truncated, full table size 1106 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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