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Sample GSM81900 Query DataSets for GSM81900
Status Public on Nov 04, 2005
Title sarc12 v 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 sarc12
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics sarc12
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23960.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 8132 8098 1011 882 7121 7216 7467 7138 1081 915 6456 6256 0 0 3860 4451 335 263 100 100 100 100 14337 12712 .987 1.013 .969 .959 .971 1.196 32 230 1.06 .99 70 750 18960 60 67 27 34 0 6427 700 5727 .804 5665 4965 1.243 .769 -.314 -.379
2 9637 11394 840 739 8797 10655 6474 7079 847 757 5634 6340 0 0 6895 8708 141 151 100 100 100 100 19452 11974 .826 1.211 1.125 1.149 1.188 1.221 52 340 1.238 .99 80 990 18960 60 68 51 59 0 9043 587 8456 .961 5618 5032 1.04 .893 -.057 -.163
3 4125 4512 810 820 3315 3692 2786 2917 895 936 1976 2097 0 0 2853 3215 344 490 96 90 93 81 7007 4073 .898 1.114 1.061 1.043 1.201 1.382 32 176 1.141 .98 60 1190 18960 61 67 72 78 0 3581 651 2930 .884 2315 1664 1.131 .842 -.178 -.248
4 13297 15844 561 516 12736 15328 8885 11035 586 545 8324 10519 0 0 7721 9909 156 186 100 100 100 100 28064 18843 .831 1.204 1.264 1.171 1.173 1.161 52 420 1.232 .99 90 1410 18950 58 67 92 101 0 12575 410 12165 .955 8758 8348 1.047 1.003 -.066 .004
5 9584 13216 496 415 9088 12801 7597 10492 495 420 7101 10077 0 0 5395 7820 78 90 100 100 100 100 21889 17178 .71 1.409 1.419 1.382 1.393 1.206 80 560 1.423 .99 100 1650 18950 58 68 116 126 0 10489 329 10160 1.118 8327 7998 .895 1.126 .161 .172
6 6520 7460 476 377 6044 7083 4330 4284 485 381 3854 3907 0 0 4630 6118 71 80 100 100 100 100 13127 7761 .853 1.172 1.014 1.079 1.071 1.228 52 332 1.245 .99 80 1870 18940 58 66 139 147 0 5921 299 5621 .93 3400 3101 1.075 .805 -.105 -.314
7 7803 9965 513 400 7290 9565 5395 8663 563 456 4882 8263 0 0 5882 7725 257 248 100 100 100 100 16855 13145 .762 1.312 1.693 1.248 1.264 1.374 32 230 1.308 .98 70 2080 18930 57 64 160 167 0 7909 317 7591 1.041 6875 6558 .96 1.343 .058 .426
8 13089 4169 535 401 12554 3768 10206 2889 539 415 9671 2488 0 0 8190 3126 93 94 100 100 100 100 16322 12159 3.332 .3 .257 .262 .254 1.376 52 340 .321 .96 80 2320 18940 58 66 184 192 0 3309 318 2990 .238 2293 1975 4.198 .204 -2.07 -2.292
9 14806 21428 529 395 14277 21033 9648 13887 541 405 9119 13492 0 0 9940 14831 83 88 100 100 100 100 35310 22611 .679 1.473 1.48 1.473 1.447 1.216 52 420 1.487 .99 90 2540 18930 56 65 205 214 0 17006 313 16693 1.169 11021 10708 .855 1.174 .226 .232
10 8952 12545 539 386 8413 12159 7880 9994 552 392 7341 9608 0 0 5174 7927 109 82 100 100 100 100 20572 16949 .692 1.445 1.309 1.409 1.41 1.182 52 412 1.475 .99 90 2760 18920 55 64 227 236 0 9956 306 9650 1.147 7932 7625 .872 1.039 .198 .055
11 2455 2661 524 397 1931 2264 1734 1928 537 395 1210 1531 0 0 1713 2099 114 87 100 96 90 96 4195 2741 .853 1.172 1.265 1.093 1.137 1.477 32 176 1.213 .96 60 2980 18930 58 64 251 257 0 2112 315 1797 .931 1530 1215 1.075 1.004 -.104 .006
12 15357 7243 512 423 14845 6820 16491 6740 521 442 15979 6317 0 0 7561 3911 91 115 100 100 100 100 21665 22296 2.177 .459 .395 .447 .452 1.292 80 552 .47 .98 100 3220 18920 55 65 273 283 0 5748 336 5413 .365 5349 5013 2.743 .314 -1.456 -1.672
13 1053 816 499 495 554 321 898 831 513 510 399 336 0 0 413 195 102 119 93 84 87 71 875 735 1.726 .579 .842 .649 .771 2.054 32 236 .529 .65 70 3440 18920 56 63 296 303 0 648 393 255 .46 660 267 2.175 .668 -1.121 -.581
14 749 922 523 557 226 365 611 661 532 586 88 104 0 0 368 653 91 158 48 40 36 28 591 192 .619 1.615 1.182 1.371 1.477 2.828 80 552 1.943 .79 100 3660 18910 54 64 317 327 -50 732 442 290 1.282 525 83 .78 .938 .358 -.092
15 763 1094 528 567 235 527 715 1058 544 609 187 491 0 0 198 358 104 204 76 82 38 53 762 678 .446 2.243 2.626 2.341 1.926 2.862 52 332 2.922 .62 80 3890 18910 55 63 341 349 0 868 450 418 1.78 840 390 .562 2.084 .832 1.059
16 768 1019 571 724 197 295 645 827 587 765 74 103 0 0 447 798 114 265 40 32 22 15 492 177 .668 1.497 1.392 1.801 1.638 2.796 80 538 1.927 .89 100 4110 18900 53 63 362 372 -50 809 575 234 1.188 656 82 .841 1.105 .249 .144
17 1019 814 867 712 152 102 935 744 912 747 68 32 0 0 351 269 364 266 15 21 7 8 254 100 1.49 .671 .471 1.034 1.115 3.254 80 552 .763 .6 100 750 19180 81 91 26 36 -50 646 565 81 .533 590 25 1.878 .373 -.909 -1.421
18 897 804 721 591 176 213 846 725 728 606 125 134 0 0 305 298 128 140 47 47 25 25 389 259 .826 1.21 1.072 .991 .977 2.697 80 560 3.09 .51 100 970 19180 81 91 48 58 -50 638 469 169 .96 575 106 1.041 .851 -.058 -.233
19 1305 1684 671 587 634 1097 1249 1407 842 1065 578 820 0 0 741 1039 611 1735 33 25 16 0 1731 1398 .578 1.73 1.419 1.447 1.473 1.732 12 104 1.918 .87 50 1210 19220 87 92 74 79 0 1337 466 871 1.373 1117 651 .728 1.126 .458 .171
20 840 975 513 458 327 517 583 506 547 538 70 48 0 0 1204 2437 300 627 18 7 8 5 844 118 .632 1.581 .686 1.064 1.143 3.472 80 560 2.017 .98 100 1420 19170 80 90 93 103 -50 774 363 410 1.255 402 38 .797 .544 .327 -.878

Total number of rows: 7680

Table truncated, full table size 1850 Kbytes.




Supplementary data files not provided
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