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Sample GSM69956 Query DataSets for GSM69956
Status Public on Aug 16, 2005
Title J99-A9-1 vs Tigr/Astra references (250 ug).
Sample type genomic
 
Channel 1
Source name 250 ng Tigr/Astra genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng Tigr/Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 250 ng J99-A9 genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng J99-A9 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18205.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 15, 2005
Last update date Sep 22, 2006
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)
GSE3137 H. pilory diversity in human

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 20475 17170 569 1057 19906 16113 21074 17716 589 1115 20505 16659 0 0 3430 3828 215 427 100 100 100 100 36019 37164 1.235 .809 .812 .788 .816 1.28 52 420 .828 .98 90 1370 12930 40 49 20 29 0 19950 1228 18721 .94 20584 19356 1.063 .944 -.089 -.083
2 11952 2580 564 983 11388 1597 12010 2552 568 1023 11446 1569 0 0 2100 651 134 309 100 97 100 95 12985 13015 7.131 .14 .137 .133 .137 1.364 80 560 .137 .87 100 1600 12930 40 50 43 53 0 2998 1142 1856 .163 2965 1823 6.137 .159 -2.618 -2.65
3 13360 12219 599 1043 12761 11176 13471 11969 632 1097 12872 10926 0 0 2016 2060 302 341 100 100 100 100 23937 23798 1.142 .876 .849 .874 .859 1.132 52 412 .879 .98 90 1830 12920 39 48 66 75 0 14197 1212 12985 1.018 13907 12695 .983 .986 .025 -.02
4 887 1448 539 1087 348 361 372 999 550 1102 -167 -88 0 0 1308 1150 111 307 23 28 22 23 709 -255 .964 1.037 null 1.102 1.109 2.216 80 648 .965 .83 110 2070 12920 38 49 89 100 -100 1682 1263 419 1.205 1161 -102 .83 null .269 null
5 768 1363 569 1096 199 267 460 1155 579 1146 -109 59 0 0 681 731 143 367 31 37 27 20 466 -50 .745 1.342 null 1.186 1.096 3.746 80 642 1.569 .7 110 2320 12920 38 49 114 125 -100 1584 1273 310 1.559 1342 69 .641 null .641 null
6 10707 6667 548 1055 10159 5612 10758 6636 563 1091 10210 5581 0 0 1671 1262 141 320 100 100 100 100 15771 15791 1.81 .552 .547 .545 .544 1.176 156 1028 .554 .97 140 2560 12920 37 51 137 151 0 7746 1226 6521 .642 7710 6484 1.558 .635 -.64 -.655
7 4019 4128 518 1032 3501 3096 2484 2740 536 1062 1966 1708 0 0 3683 3148 168 310 77 78 73 67 6597 3674 1.131 .884 .869 .898 .864 2.181 80 642 .866 .98 110 2800 12920 38 49 162 173 -100 4796 1199 3597 1.027 3184 1985 .973 1.009 .039 .014
8 1877 2287 479 1005 1398 1282 589 1456 501 1046 110 451 0 0 2378 1977 145 309 47 56 38 38 2680 561 1.09 .917 4.1 1.162 .994 2.785 80 648 .865 .94 110 3040 12920 38 49 186 197 -100 2657 1168 1490 1.065 1692 524 .939 4.764 .092 2.252
9 10184 8676 429 973 9755 7703 10331 8645 437 995 9902 7672 0 0 1993 1916 99 271 100 100 100 100 17458 17574 1.266 .79 .775 .782 .798 1.143 52 412 .798 .97 90 3280 12920 39 48 211 220 0 10081 1131 8950 .917 10045 8914 1.09 .9 -.124 -.152
10 950 1607 366 890 584 717 409 1106 376 915 43 216 0 0 1466 1559 84 274 45 43 31 25 1301 259 .815 1.228 5.023 1.658 1.521 2.97 80 648 1.145 .89 110 3520 12920 38 49 234 245 -100 1867 1034 833 1.426 1285 251 .701 5.836 .512 2.545
11 1389 1767 334 846 1055 921 743 1389 346 874 409 543 0 0 1316 1126 90 282 76 62 68 47 1976 952 1.145 .873 1.328 1.184 .988 3.021 80 648 .903 .88 110 3760 12920 38 49 258 269 -100 2053 983 1070 1.014 1614 631 .986 1.543 .021 .625
12 5692 1581 301 826 5391 755 5599 1538 314 833 5298 712 0 0 760 427 110 251 100 91 100 68 6146 6010 7.14 .14 .134 .121 .135 1.824 156 1105 .15 .76 150 4020 12920 36 51 282 297 0 1837 960 877 .163 1787 827 6.146 .156 -2.62 -2.679
13 4939 8865 282 818 4657 8047 4863 8596 296 844 4581 7778 0 0 1485 2964 101 299 100 100 100 100 12704 12359 .579 1.728 1.698 1.689 1.715 1.293 156 1104 1.838 .96 150 4250 12930 37 52 305 320 0 10300 950 9350 2.008 9988 9037 .498 1.973 1.006 .98
14 4972 4960 308 822 4664 4138 4951 4888 311 862 4643 4066 0 0 1437 1327 80 293 100 100 100 100 8802 8709 1.127 .887 .876 .887 .909 1.227 52 332 .874 .96 80 4490 12920 40 48 333 341 0 5763 955 4808 1.031 5679 4724 .97 1.017 .044 .025
15 1131 1866 290 806 841 1060 412 1488 299 843 122 682 0 0 1500 1338 65 302 56 65 48 55 1901 804 .793 1.26 5.59 2.9 2.901 4.262 80 656 1.064 .5 110 4730 12930 39 50 355 366 -100 2168 936 1232 1.464 1729 792 .683 6.495 .55 2.699
16 1314 2794 291 919 1023 1875 726 2284 299 1014 435 1365 0 0 1448 1768 66 417 77 80 68 70 2898 1800 .546 1.833 3.138 2.79 2.405 2.346 80 656 1.594 .82 110 4970 12930 39 50 379 390 -100 3246 1068 2179 2.13 2654 1586 .47 3.646 1.091 1.866
17 1209 2002 317 870 892 1132 1038 1878 321 952 721 1008 0 0 874 1065 65 378 85 73 77 56 2024 1729 .788 1.269 1.398 1.405 1.3 2.162 80 656 1.381 .86 110 5210 12930 39 50 403 414 -100 2326 1011 1315 1.475 2182 1171 .678 1.624 .56 .7
18 1404 3249 551 1067 853 2182 675 1733 563 1080 124 666 0 0 1597 3074 115 297 52 67 41 53 3035 790 .391 2.558 5.371 3.163 3.769 2.51 80 656 2.35 .83 110 1350 13160 62 73 17 28 -100 3775 1240 2535 2.972 2014 774 .336 6.24 1.572 2.642
19 4104 4108 552 1024 3552 3084 3581 3647 563 1035 3029 2623 0 0 2444 2274 114 282 94 92 94 88 6636 5652 1.152 .868 .866 .864 .856 1.594 52 340 .89 .96 80 1600 13160 64 72 44 52 0 4773 1190 3583 1.009 4237 3048 .991 1.006 .013 .009
20 1250 1690 510 1035 740 655 883 1373 531 1070 373 338 0 0 945 904 163 350 56 50 52 41 1395 711 1.13 .885 .906 .999 .966 2.573 80 640 1.104 .79 110 1830 13160 62 73 65 76 -100 1964 1203 761 1.028 1595 393 .972 1.053 .04 .074

Total number of rows: 4608

Table truncated, full table size 1105 Kbytes.




Supplementary data files not provided
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