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Sample GSM184305 Query DataSets for GSM184305
Status Public on Aug 09, 2007
Title 259a3 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 259a3
Organism Helicobacter pylori
Characteristics 0.25 ug 259a3
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/2002-08/32415.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 7172 10866 611 1048 6561 9818 7907 11775 772 1238 7296 10727 0 0 4398 6910 570 725 96 96 93 93 16379 18023 .668 1.496 1.47 1.469 1.472 1.128 32 190 1.508 .99 70 1130 11980 114 121 109 116 0 9702 936 8766 1.336 10513 9578 .748 1.313 .418 .393
2 4198 2433 569 951 3629 1482 3382 1252 573 966 2813 301 0 0 2792 1829 75 114 100 56 100 53 5111 3114 2.449 .408 .107 .284 .422 4.732 32 236 .416 .66 70 1370 11980 114 121 133 140 0 2172 849 1323 .365 1118 269 2.743 .096 -1.456 -3.388
3 9761 12610 557 964 9204 11646 10500 12871 559 953 9943 11907 0 0 5540 6790 88 161 100 100 100 100 20850 21850 .79 1.265 1.198 1.266 1.242 1.165 32 236 1.258 1 70 1610 11980 114 121 157 164 0 11259 861 10398 1.13 11492 10631 .885 1.069 .176 .097
4 694 1400 521 880 173 520 467 813 725 1389 -54 -67 0 0 482 1290 1173 2888 7 9 0 0 693 -121 .333 3.006 null 1.982 2.284 1.995 52 420 2.459 .93 90 1870 11970 112 121 182 191 0 1250 786 464 2.684 726 null .373 null 1.424 null
5 754 1560 519 872 235 688 564 960 525 867 45 88 0 0 485 1348 61 110 46 46 38 42 923 133 .342 2.928 1.956 1.648 1.959 2.47 52 420 2.933 .92 90 2110 11970 112 121 206 215 0 1393 779 614 2.614 857 79 .383 1.746 1.386 .804
6 9368 5477 552 899 8816 4578 7727 4689 556 914 7175 3790 0 0 7851 4332 83 164 94 82 92 82 13394 10965 1.926 .519 .528 .483 .504 2.084 52 420 .53 .99 90 2350 11970 112 121 230 239 0 4890 803 4088 .464 4187 3384 2.157 .472 -1.109 -1.084
7 847 1580 495 788 352 792 537 841 493 803 42 53 0 0 656 1813 96 219 40 37 37 31 1144 95 .444 2.25 1.262 1.743 1.598 2.401 32 236 2.962 .91 70 2570 11970 113 120 253 260 0 1411 704 707 2.009 751 47 .498 1.127 1.006 .172
8 617 1034 481 784 136 250 407 594 481 791 -74 -190 0 0 396 929 56 99 38 34 32 34 386 -264 .544 1.838 null 2.157 2.192 2.191 52 340 2.464 .9 80 2830 11970 113 121 279 287 0 923 700 223 1.641 530 null .609 null .715 null
9 3556 4798 525 889 3031 3909 2250 3030 528 900 1725 2141 0 0 2817 3840 64 123 100 98 96 92 6940 3866 .775 1.29 1.241 1.143 1.225 1.438 52 340 1.336 .99 80 3070 11970 113 121 303 311 0 4284 794 3490 1.151 2705 1912 .868 1.108 .204 .148
10 906 1583 543 922 363 661 680 953 544 922 137 31 0 0 622 1367 65 120 55 46 51 40 1024 168 .549 1.821 .226 1.541 1.817 2.53 52 340 2.286 .9 80 3310 11970 113 121 327 335 0 1413 823 590 1.626 851 28 .615 .202 .701 -2.307
11 916 1819 542 883 374 936 520 903 549 899 -22 20 0 0 871 2172 84 185 34 40 28 28 1310 -2 .4 2.503 null 2.05 2.245 2.219 52 340 2.545 .97 80 3550 11970 113 121 351 359 0 1624 788 836 2.235 806 18 .448 null 1.16 null
12 4735 5437 555 935 4180 4502 4984 5117 557 944 4429 4182 0 0 3250 3555 64 128 98 94 98 84 8682 8611 .928 1.077 .944 .997 1.051 1.585 52 340 1.07 .99 80 3790 11970 113 121 375 383 0 4854 835 4020 .962 4569 3734 1.04 .843 -.056 -.246
13 2187 2487 559 969 1628 1518 2242 2316 564 967 1683 1347 0 0 1323 1446 71 130 87 71 81 65 3146 3030 1.072 .932 .8 .746 .803 1.957 32 230 1.039 .95 70 4030 11960 112 119 399 406 0 2221 865 1355 .833 2068 1203 1.201 .715 -.264 -.485
14 5371 11700 597 1014 4774 10686 5595 12627 602 1044 4998 11613 0 0 3002 6764 87 192 100 100 100 100 15460 16611 .447 2.238 2.324 2.218 2.189 1.176 32 230 2.241 1 70 4270 11960 112 119 423 430 0 10446 905 9541 1.999 11274 10369 .5 2.075 .999 1.053
15 2360 5160 565 917 1795 4243 2119 4788 559 912 1554 3871 0 0 1599 3619 83 145 78 81 78 81 6038 5425 .423 2.364 2.491 2.597 2.552 1.31 32 230 2.327 .99 70 4510 11960 112 119 447 454 0 4607 819 3788 2.111 4275 3456 .474 2.224 1.078 1.153
16 1456 2193 614 1034 842 1159 847 1057 615 1033 233 23 0 0 1133 1779 68 120 78 50 71 40 2001 256 .726 1.376 .099 1.868 1.653 2.99 32 230 1.592 .93 70 4750 11960 112 119 471 478 0 1958 923 1035 1.229 944 21 .814 .088 .297 -3.504
17 2035 3344 625 1088 1410 2256 1285 1677 630 1095 660 589 0 0 1760 3231 63 119 100 87 96 84 3666 1249 .625 1.6 .892 1.044 .995 1.951 32 230 1.807 .97 70 4990 11960 112 119 495 502 0 2986 971 2014 1.429 1497 526 .7 .797 .515 -.328
18 3636 4729 590 961 3046 3768 2703 4309 593 975 2113 3348 0 0 2600 2845 76 154 93 93 93 87 6814 5461 .808 1.237 1.584 1.328 1.259 1.523 32 236 1.187 .98 70 1170 12220 138 145 113 120 0 4222 858 3364 1.104 3847 2989 .905 1.415 .143 .501
19 4388 5437 577 1000 3811 4437 4187 5336 673 1047 3610 4336 0 0 1990 2759 380 259 100 100 100 100 8248 7946 .859 1.164 1.201 1.02 1.139 1.453 52 340 1.284 .96 80 1410 12200 136 144 137 145 0 4854 893 3962 1.04 4764 3871 .962 1.072 .056 .101
20 1046 1709 540 906 506 803 1014 1552 529 890 474 646 0 0 678 1406 80 167 57 51 57 51 1309 1120 .63 1.587 1.363 1.798 2.148 2.061 52 340 2.058 .9 80 1650 12200 136 144 161 169 0 1526 809 717 1.417 1386 577 .706 1.217 .503 .283

Total number of rows: 4608

Table truncated, full table size 1105 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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