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Sample GSM184250 Query DataSets for GSM184250
Status Public on Aug 09, 2007
Title 251c5 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 251c5 genomic DNA
Organism Helicobacter pylori
Characteristics 0.25 ug 251c5 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/2002-07/30941.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 7790 8684 236 542 7554 8142 5427 6296 281 578 5191 5754 0 0 5842 6203 309 325 96 98 92 96 15696 10945 .928 1.078 1.108 1.142 1.103 1.28 52 420 1.068 .99 90 2320 40750 119 128 100 109 0 11426 713 10713 1.418 8284 7571 .705 1.458 .504 .544
2 4304 1201 234 531 4070 670 3057 901 241 549 2823 370 0 0 4374 872 53 157 96 75 96 53 4740 3193 6.075 .165 .131 .156 .133 2.347 52 340 .137 .71 80 2530 40750 120 128 122 130 0 1580 699 882 .217 1186 487 4.617 .172 -2.207 -2.536
3 8845 5896 240 523 8605 5373 5197 3279 250 525 4957 2756 0 0 8098 4984 59 145 100 100 100 100 13978 7713 1.602 .624 .556 .615 .606 1.287 52 420 .614 .99 90 2790 40750 119 128 147 156 0 7758 688 7070 .822 4314 3626 1.217 .732 -.284 -.451
4 310 606 230 555 80 51 257 555 237 555 27 0 0 0 180 284 45 168 30 23 18 10 131 27 1.569 .638 null 3.679 4.091 3.663 80 560 2.666 .68 100 3030 40730 117 127 171 181 -100 797 730 67 .839 730 0 1.192 null -.254 null
5 290 623 225 534 65 89 233 572 248 594 8 38 0 0 154 330 235 607 12 3 3 2 154 46 .73 1.369 4.75 2.529 2.107 3.458 80 560 4.469 .5 100 3270 40730 117 127 195 205 -100 820 703 117 1.802 753 50 .555 6.25 .849 2.644
6 3130 3835 239 578 2891 3257 1345 2096 249 596 1106 1518 0 0 4422 4852 88 205 68 71 63 60 6148 2624 .888 1.127 1.373 1.621 1.135 2.465 80 560 1.075 .99 100 3510 40730 117 127 219 229 -100 5046 761 4286 1.482 2758 1997 .675 1.806 .568 .853
7 1077 1409 242 599 835 810 787 1164 250 611 545 565 0 0 664 782 97 161 100 88 100 72 1645 1110 1.031 .97 1.037 .849 .94 1.784 80 560 1.096 .89 100 3750 40730 117 127 243 253 -100 1854 788 1066 1.276 1532 743 .783 1.364 .352 .448
8 371 776 238 611 133 165 283 673 249 640 45 62 0 0 239 451 137 320 26 20 16 8 298 107 .806 1.241 1.378 2.096 1.833 4.704 80 560 2.54 .85 100 3990 40730 117 127 267 277 -100 1021 804 217 1.632 886 82 .613 1.813 .707 .858
9 3747 3222 241 618 3506 2604 3382 2754 246 619 3141 2136 0 0 2029 1549 69 169 100 98 98 97 6110 5277 1.346 .743 .68 .742 .718 1.395 80 560 .745 .96 100 4240 40750 119 129 292 302 0 4239 813 3426 .977 3624 2811 1.023 .895 -.033 -.16
10 1056 1601 284 627 772 974 1094 1400 313 670 810 773 0 0 317 663 105 191 100 91 100 91 1746 1583 .793 1.262 .954 1.124 1.04 1.937 12 104 1.788 .7 50 4470 40730 119 124 317 322 0 2107 825 1282 1.66 1842 1017 .602 1.256 .731 .328
11 454 917 243 635 211 282 291 732 245 641 48 97 0 0 331 604 43 167 52 37 38 23 493 145 .748 1.336 2.021 1.699 1.591 3.185 80 552 1.978 .76 100 4710 40720 116 126 339 349 -50 1207 836 371 1.759 963 128 .569 2.659 .814 1.411
12 4351 1127 258 630 4093 497 3947 893 260 641 3689 263 0 0 2831 723 46 167 100 55 100 44 4590 3952 8.235 .121 .071 .116 .106 2.22 52 340 .118 .61 80 4940 40750 120 128 363 371 0 1483 829 654 .16 1175 346 6.259 .094 -2.646 -3.414
13 2473 2708 251 614 2222 2094 2238 2423 289 676 1987 1809 0 0 1272 1325 853 1155 87 75 65 36 4316 3796 1.061 .942 .91 .954 .883 1.613 120 820 .982 .96 120 5190 40730 116 128 386 398 0 3563 808 2755 1.24 3188 2380 .806 1.198 .31 .261
14 8867 7647 275 666 8592 6981 7341 7027 281 681 7066 6361 0 0 5725 4491 60 191 100 98 100 96 15573 13427 1.231 .813 .9 .825 .802 1.229 52 340 .798 .99 80 5440 40740 119 127 413 421 0 10062 876 9186 1.069 9246 8370 .935 1.185 .096 .244
15 2163 2278 261 599 1902 1679 1650 1746 264 613 1389 1147 0 0 1492 1484 51 164 100 92 100 86 3581 2536 1.133 .883 .826 .801 .875 1.757 52 340 .936 .92 80 5680 40730 118 126 437 445 0 2997 788 2209 1.162 2297 1509 .861 1.087 .216 .12
16 1021 1620 254 634 767 986 821 1116 265 632 567 482 0 0 953 1259 64 153 78 75 75 59 1753 1049 .778 1.286 .85 1.04 1.061 2.869 32 176 1.513 .8 60 5930 40730 119 125 463 469 0 2132 834 1297 1.691 1468 634 .591 1.119 .758 .162
17 1010 1519 263 677 747 842 806 1286 338 734 543 609 0 0 768 851 316 383 59 65 43 40 1589 1152 .887 1.127 1.122 1.421 1.143 2.654 32 236 1.021 .95 70 6150 40730 118 125 484 491 0 1999 891 1108 1.483 1692 801 .674 1.476 .569 .561
18 2812 2164 235 609 2577 1555 1391 1151 265 631 1156 542 0 0 3673 2080 109 210 100 87 100 59 4132 1698 1.657 .603 .469 .505 .573 2.257 32 236 .567 .95 70 2320 41000 145 152 101 108 0 2847 801 2046 .794 1514 713 1.259 .617 -.333 -.697
19 4465 3470 229 522 4236 2948 3678 2740 236 531 3449 2218 0 0 2920 2239 46 152 100 99 100 99 7184 5667 1.437 .696 .643 .671 .688 1.25 120 801 .719 .98 120 2570 40960 139 151 124 136 0 4566 687 3879 .916 3605 2918 1.092 .846 -.127 -.241
20 770 992 250 508 520 484 631 755 251 525 381 247 0 0 342 603 40 156 96 68 96 40 1004 628 1.074 .931 .648 .715 .829 3.767 32 176 1.959 .66 60 2810 40970 143 149 151 157 0 1305 668 637 1.225 993 325 .817 .853 .292 -.229

Total number of rows: 4608

Table truncated, full table size 1102 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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