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Sample GSM81866 Query DataSets for GSM81866
Status Public on Nov 04, 2005
Title sarb12 vs. SL1344 1
Sample type genomic
 
Channel 1
Source name SL1344
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics SL1344
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name sarb12
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics sarb12
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22865.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 Nov 03, 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 GPL3048
Series (1)
GSE3564 Genomic comparison of Salmonella enterica serovars and Salmonella bongori

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 4111 3649 744 639 3367 3010 3487 2994 755 639 2743 2355 0 0 2272 2046 99 75 100 100 100 100 6377 5098 1.119 .894 .859 .901 .892 1.318 32 236 .897 .98 70 1380 19170 53 60 70 77 0 4688 821 3867 1.148 3846 3025 .871 1.103 .2 .141
2 3555 3002 713 614 2842 2388 1917 1569 714 619 1204 955 0 0 3287 2707 82 68 98 98 98 96 5230 2159 1.19 .84 .793 .831 .845 1.625 80 552 .825 .99 100 1620 19160 51 61 93 103 0 3857 789 3068 1.079 2016 1227 .926 1.019 .11 .027
3 2447 2089 712 608 1735 1481 2210 1853 713 612 1498 1245 0 0 1255 1024 86 67 96 100 93 96 3216 2743 1.172 .854 .831 .866 .889 1.299 32 236 .836 .97 70 1840 19160 52 59 116 123 0 2684 781 1903 1.097 2380 1599 .912 1.068 .133 .094
4 4387 3467 736 642 3651 2825 2370 1922 745 650 1634 1280 0 0 3891 2970 98 84 99 99 97 98 6476 2914 1.292 .774 .783 .799 .786 1.39 120 865 .765 .99 130 2040 19170 50 63 133 146 0 4454 825 3629 .994 2469 1644 1.006 1.006 -.009 .009
5 5814 4635 735 640 5079 3995 4766 4004 752 654 4031 3364 0 0 3781 2963 112 102 100 100 100 98 9074 7395 1.271 .787 .835 .77 .767 1.311 80 650 .784 .99 110 2300 19180 52 63 160 171 0 5954 822 5132 1.01 5144 4322 .99 1.072 .015 .1
6 3850 3328 696 604 3154 2724 2293 1769 704 615 1597 1165 0 0 3282 2828 103 102 100 100 98 98 5878 2762 1.158 .864 .729 .842 .853 1.342 52 340 .863 .99 80 2510 19170 53 61 183 191 0 4275 776 3499 1.11 2273 1497 .901 .937 .15 -.094
7 2545 2272 710 610 1835 1662 1352 1114 733 666 642 504 0 0 2178 2064 130 216 95 83 81 55 3497 1146 1.104 .906 .785 .859 .858 1.761 80 642 .932 .97 110 2740 19170 51 62 204 215 0 2919 784 2135 1.164 1431 647 .859 1.009 .219 .012
8 5884 4528 710 603 5174 3925 4172 3020 709 605 3462 2417 0 0 4316 3388 87 73 100 100 100 100 9099 5879 1.318 .759 .698 .723 .744 1.22 52 340 .769 .99 80 2970 19170 53 61 229 237 0 5817 775 5042 .975 3880 3105 1.026 .897 -.037 -.157
9 5694 4642 710 595 4984 4047 3730 2854 717 607 3020 2259 0 0 4308 3598 128 104 100 100 100 100 9031 5279 1.232 .812 .748 .765 .785 1.26 52 420 .819 .99 90 3200 19170 52 61 251 260 0 5963 764 5199 1.043 3666 2902 .959 .961 .061 -.057
10 5166 4589 706 591 4460 3998 4076 3716 881 748 3370 3125 0 0 3137 2889 1519 1125 84 96 53 61 8458 6495 1.116 .896 .927 .888 .885 1.27 52 420 .902 .99 90 3420 19170 52 61 273 282 0 5895 759 5136 1.152 4774 4015 .868 1.191 .204 .252
11 1708 1431 692 590 1016 841 1392 1314 692 594 700 724 0 0 798 636 85 72 96 100 90 96 1857 1424 1.208 .828 1.034 .889 .853 1.537 32 176 .806 .95 60 3630 19170 54 60 296 302 0 1838 758 1080 1.063 1688 930 .94 1.329 .089 .41
12 6401 4796 731 620 5670 4176 6977 5179 751 651 6246 4559 0 0 3873 2852 250 317 97 93 95 87 9846 10805 1.358 .737 .73 .747 .744 1.465 80 650 .74 .99 110 3860 19160 50 61 316 327 0 6161 796 5365 .946 6653 5857 1.057 .938 -.08 -.093
13 1745 1778 701 579 1044 1199 1536 1666 709 587 835 1087 0 0 983 1031 107 91 84 84 84 84 2243 1922 .871 1.148 1.302 1.209 1.076 1.739 32 236 1.113 .93 70 4090 19180 54 61 341 348 0 2284 744 1540 1.475 2140 1396 .678 1.672 .561 .742
14 1587 1694 689 565 898 1129 1125 1126 691 567 436 561 0 0 814 992 86 59 93 93 90 90 2027 997 .795 1.257 1.287 1.226 1.25 2.057 32 176 1.248 .96 60 4310 19180 55 61 364 370 0 2176 726 1450 1.615 1447 721 .619 1.653 .692 .725
15 1240 1441 698 591 542 850 1221 1524 701 597 523 933 0 0 719 860 93 71 75 75 67 75 1392 1456 .638 1.568 1.784 1.525 1.433 2.251 52 414 1.318 .9 90 4530 19180 53 62 384 393 0 1851 759 1092 2.015 1958 1199 .496 2.292 1.011 1.196
16 774 681 675 581 99 100 740 639 681 586 65 58 0 0 202 169 90 72 47 46 16 20 199 123 .99 1.01 .892 .793 .839 3.197 80 552 .707 .53 100 4750 19160 51 61 406 416 -50 875 746 128 1.298 821 75 .771 1.146 .376 .197
17 2931 3148 816 712 2115 2436 2878 3283 837 716 2062 2571 0 0 1092 1309 145 109 98 98 98 98 4551 4633 .868 1.152 1.247 1.104 1.178 1.695 52 340 1.177 .94 80 1390 19380 74 82 71 79 0 4044 915 3129 1.48 4218 3303 .676 1.602 .565 .68
18 2083 2430 744 612 1339 1818 1834 2392 749 615 1090 1780 0 0 820 1153 92 74 100 96 96 96 3157 2870 .737 1.358 1.633 1.158 1.331 2.082 32 236 1.396 .94 70 1620 19380 74 81 94 101 0 3122 786 2336 1.744 3073 2287 .573 2.098 .803 1.069
19 820 748 709 605 111 143 748 680 717 606 39 75 0 0 250 256 86 70 36 51 20 27 254 114 .776 1.288 1.923 1.335 1.303 3.312 80 554 1.012 .69 100 1830 19380 73 83 114 124 -50 961 777 184 1.655 874 96 .604 2.471 .727 1.305
20 774 698 719 613 55 85 751 670 732 623 32 57 0 0 172 179 113 90 13 33 7 21 140 89 .647 1.545 1.781 1.678 1.815 3.684 80 547 .931 .57 100 2060 19380 73 83 137 147 -50 897 787 109 1.985 861 73 .504 2.288 .989 1.194

Total number of rows: 7680

Table truncated, full table size 1776 Kbytes.




Supplementary data files not provided
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