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Sample GSM81858 Query DataSets for GSM81858
Status Public on Nov 04, 2005
Title sarb16 vs. SL1344 3
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 sarb16
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics sarb16
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22861.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 1633 1930 422 583 1211 1347 1353 1882 426 585 931 1299 0 0 813 836 53 50 100 100 100 100 2558 2230 .899 1.112 1.395 1.136 1.157 1.481 32 230 1.095 .94 70 1290 17410 85 92 49 56 0 2838 857 1981 1.636 2768 1910 .611 2.052 .71 1.037
2 2075 1995 417 586 1658 1409 1077 1461 432 589 660 875 0 0 1546 1294 144 70 96 100 82 98 3067 1535 1.177 .85 1.326 .922 .875 1.74 52 340 .834 .95 80 1510 17410 85 93 71 79 0 2934 862 2072 1.25 2149 1287 .8 1.95 .322 .963
3 1547 1767 444 585 1103 1182 1478 1834 444 585 1034 1249 0 0 758 541 70 51 100 100 100 100 2285 2283 .933 1.072 1.208 1.245 1.259 1.403 12 104 .861 .91 50 1740 17400 85 90 95 100 0 2599 860 1738 1.576 2697 1837 .635 1.776 .656 .829
4 2419 2263 480 673 1939 1590 1788 1747 487 679 1308 1074 0 0 1651 1276 75 68 97 100 97 98 3529 2382 1.219 .82 .821 .872 .816 1.388 80 650 .79 .97 110 1980 17400 82 93 116 127 0 3328 990 2338 1.206 2569 1579 .829 1.208 .27 .272
5 2951 2823 483 700 2468 2123 2913 2411 655 1056 2430 1711 0 0 1559 1382 930 1995 73 48 55 11 4591 4141 1.163 .86 .704 .858 .888 1.364 52 420 .913 .95 90 2210 17410 84 93 140 149 0 4151 1029 3122 1.265 3546 2516 .791 1.035 .339 .05
6 1942 1956 475 735 1467 1221 1782 1668 476 730 1307 933 0 0 925 831 63 63 100 100 100 100 2688 2240 1.201 .832 .714 .795 .872 1.418 32 236 .86 .96 70 2420 17400 84 91 162 169 0 2876 1081 1796 1.224 2453 1372 .817 1.05 .292 .07
7 1733 1712 479 727 1254 985 932 1088 481 727 453 361 0 0 1419 1048 58 59 100 100 100 96 2239 814 1.273 .785 .797 .773 .749 1.677 52 420 .754 .95 90 2660 17400 83 92 185 194 0 2518 1069 1449 1.155 1600 531 .866 1.172 .208 .229
8 2570 2300 486 744 2084 1556 1724 1669 487 740 1238 925 0 0 2001 1442 59 57 98 100 96 100 3640 2163 1.339 .747 .747 .775 .799 1.462 52 340 .726 .96 80 2890 17390 83 91 209 217 0 3382 1094 2288 1.098 2454 1360 .911 1.099 .135 .136
9 2670 2428 486 721 2184 1707 2058 1798 487 722 1572 1077 0 0 1607 1361 59 59 100 100 100 100 3891 2649 1.279 .782 .685 .761 .753 1.398 52 420 .803 .95 90 3100 17390 82 91 229 238 0 3571 1060 2510 1.149 2644 1584 .87 1.008 .201 .011
10 2073 2088 507 747 1566 1341 1455 1521 508 750 948 774 0 0 1350 1150 62 60 100 100 100 100 2907 1722 1.168 .856 .816 .862 .874 1.412 52 340 .852 .96 80 3330 17390 83 91 253 261 0 3071 1099 1972 1.259 2237 1138 .794 1.201 .333 .264
11 965 1135 546 796 419 339 853 1036 544 794 307 240 0 0 388 306 72 59 75 87 68 65 758 547 1.236 .809 .782 .936 .805 1.959 32 176 .816 .93 60 3560 17390 84 90 277 283 0 1669 1171 499 1.19 1524 353 .84 1.15 .251 .201
12 2561 2241 481 740 2080 1501 2561 2261 491 744 2080 1521 0 0 735 415 69 70 100 100 100 100 3581 3601 1.386 .722 .731 .738 .719 1.197 52 420 .692 .97 90 3780 17380 81 90 297 306 0 3296 1088 2207 1.061 3325 2237 .942 1.075 .086 .105
13 839 931 473 730 366 201 734 871 475 729 261 141 0 0 323 221 58 53 90 75 81 65 567 402 1.821 .549 .54 .685 .689 3.116 32 176 .531 .7 60 4010 17380 83 89 322 328 0 1369 1074 296 .808 1281 207 1.238 .794 -.308 -.332
14 547 790 474 748 73 42 519 782 478 750 45 34 0 0 136 79 53 54 42 32 21 12 115 79 1.738 .575 .756 .825 .735 3.528 80 552 .278 .17 100 4230 17370 80 90 342 352 -50 1162 1100 62 .846 1150 50 1.182 1.111 -.241 .152
15 589 801 472 735 117 66 520 767 475 736 48 32 0 0 189 140 55 57 46 36 37 17 183 80 1.773 .564 .667 .777 .617 3.799 80 552 .665 .64 100 4460 17370 80 90 365 375 -50 1178 1081 97 .83 1128 47 1.205 .98 -.27 -.029
16 500 739 475 744 25 -5 483 741 477 741 8 -3 0 0 79 67 54 56 27 18 12 3 20 5 null null null .896 .796 4.151 80 552 .828 .19 100 4680 17370 80 90 387 397 -50 1087 1094 -7 null 1090 null null null null null
17 938 1460 431 606 507 854 934 1526 432 612 503 920 0 0 299 271 61 51 100 100 83 100 1361 1423 .594 1.684 1.829 2.056 1.806 1.887 12 104 1.539 .88 50 1310 17620 107 112 52 57 0 2147 891 1256 2.477 2244 1353 .404 2.69 1.309 1.427
18 786 1253 419 597 367 656 810 1253 421 601 391 656 0 0 242 309 55 48 91 100 83 100 1023 1047 .559 1.787 1.678 2.238 1.977 2.293 12 104 1.767 .84 50 1530 17630 108 113 74 79 0 1843 878 965 2.629 1843 965 .38 2.467 1.394 1.303
19 441 613 448 623 -7 -10 429 611 451 631 -19 -12 0 0 68 62 58 63 13 11 8 2 -17 -31 null null null 1.312 1.208 3.551 80 560 1.01 .23 100 1750 17620 105 115 94 104 -50 901 916 -15 null 899 null null null null null
20 477 680 495 695 -18 -15 478 676 499 694 -17 -19 0 0 70 58 65 61 13 12 2 0 -33 -36 null null null .713 .737 2.925 80 560 .351 .13 100 1970 17620 105 115 116 126 -50 1000 1022 -22 null 994 null null null null null

Total number of rows: 7680

Table truncated, full table size 1738 Kbytes.




Supplementary data files not provided
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