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Sample GSM81881 Query DataSets for GSM81881
Status Public on Nov 04, 2005
Title sarc11 vs. SL1344 2
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 sarc11
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics sarc11
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22852.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 2351 3847 774 702 1577 3145 1617 2125 774 703 843 1423 0 0 1807 4153 94 64 98 100 94 98 4722 2266 .501 1.994 1.688 1.718 1.72 2.071 52 340 2.272 .94 80 1840 17430 75 83 72 80 0 2565 468 2097 1.33 1417 949 .752 1.125 .411 .17
2 3398 8204 735 691 2663 7513 2360 5320 740 690 1625 4629 0 0 2114 5850 93 74 98 100 98 100 10176 6254 .354 2.821 2.849 2.78 2.842 1.529 52 420 2.888 .96 90 2060 17420 73 82 93 102 0 5469 461 5009 1.881 3547 3086 .532 1.899 .911 .925
3 1571 3779 666 609 905 3170 1335 2414 878 622 669 1805 0 0 827 3008 2668 126 3 100 0 100 4075 2474 .285 3.503 2.698 3.621 2.87 2.075 32 176 3.938 .89 60 2280 17440 77 83 117 123 0 2519 406 2113 2.335 1609 1203 .428 1.799 1.224 .847
4 4421 9756 785 802 3636 8954 3261 6669 938 1010 2476 5867 0 0 3254 7000 1582 1220 61 93 42 83 12590 8343 .406 2.463 2.37 2.951 2.588 1.981 80 650 1.983 .84 110 2510 17420 72 83 137 148 0 6504 535 5969 1.642 4446 3911 .609 1.58 .715 .66
5 4274 8784 811 881 3463 7903 2961 5333 825 937 2150 4452 0 0 3179 6894 122 249 91 97 88 96 11366 6602 .438 2.282 2.071 2.192 2.247 1.692 80 560 2.326 .93 100 2740 17430 74 84 161 171 0 5856 587 5269 1.521 3555 2968 .657 1.38 .605 .465
6 2625 7151 777 817 1848 6334 1659 3647 787 835 882 2830 0 0 1797 6313 101 100 98 100 96 100 8182 3712 .292 3.427 3.209 3.342 3.092 1.641 52 420 3.683 .92 90 2960 17430 74 83 183 192 0 4767 545 4223 2.285 2431 1887 .438 2.139 1.192 1.097
7 2317 5610 765 813 1552 4797 1452 2799 771 819 687 1986 0 0 1806 5353 99 89 98 100 94 100 6349 2673 .324 3.091 2.891 3.284 3.213 1.902 52 340 3.154 .94 80 3190 17430 75 83 207 215 0 3740 542 3198 2.061 1866 1324 .485 1.927 1.043 .947
8 3535 4814 763 862 2772 3952 2506 2595 778 865 1743 1733 0 0 2784 4170 98 93 98 100 98 100 6724 3476 .701 1.426 .994 1.269 1.26 1.564 52 340 1.523 .9 80 3410 17430 75 83 229 237 0 3209 575 2635 .95 1730 1155 1.052 .663 -.073 -.593
9 4123 11340 786 898 3337 10442 2799 8127 788 907 2013 7229 0 0 3043 7736 97 96 96 100 92 100 13779 9242 .32 3.129 3.591 3.695 3.06 1.863 52 420 2.933 .95 90 3630 17430 74 83 250 259 0 7560 599 6961 2.086 5418 4819 .479 2.394 1.061 1.259
10 3312 7759 789 931 2523 6828 2674 5866 792 938 1885 4935 0 0 1769 4483 105 120 100 100 100 100 9351 6820 .37 2.706 2.618 2.784 2.653 1.442 52 420 2.734 .94 90 3870 17440 75 84 274 283 0 5173 621 4552 1.804 3911 3290 .554 1.745 .851 .804
11 2286 5432 788 941 1498 4491 2356 5533 798 955 1568 4592 0 0 1148 2289 112 139 91 100 66 100 5989 6160 .334 2.998 2.929 3.607 3.903 1.797 12 104 2.778 .89 50 4100 17430 76 81 299 304 0 3621 627 2994 1.999 3689 3061 .5 1.952 .999 .965
12 5607 5653 830 1025 4777 4628 5327 5223 830 1023 4497 4198 0 0 1473 1945 97 90 100 100 100 100 9405 8695 1.032 .969 .934 .926 .955 1.328 52 340 .992 .95 80 4310 17440 76 84 319 327 0 3769 683 3085 .646 3482 2799 1.548 .622 -.631 -.684
13 1275 1687 816 979 459 708 1142 1582 826 1033 326 603 0 0 449 697 143 326 75 62 56 43 1167 929 .648 1.542 1.85 1.386 1.563 2.288 32 176 2.035 .76 60 4530 17440 77 83 342 348 0 1125 653 472 1.028 1055 402 .972 1.233 .04 .302
14 852 1193 793 942 59 251 770 965 799 943 -23 23 0 0 249 597 111 94 25 36 16 22 310 0 .235 4.254 null .885 1.064 5.188 80 552 3.48 .5 100 4750 17420 73 83 362 372 -50 795 628 167 2.836 643 15 .353 null 1.504 null
15 1257 1831 792 1036 465 795 1200 1757 816 1030 408 721 0 0 344 563 104 97 83 91 75 91 1260 1129 .585 1.71 1.767 2.423 2.277 2.104 12 104 1.58 .7 50 4970 17440 77 82 386 391 0 1221 691 530 1.14 1171 481 .877 1.178 .189 .236
16 874 1183 821 1026 53 157 818 1019 824 1039 -3 -7 0 0 285 576 105 104 17 22 10 16 210 -10 .338 2.962 null 1.21 1.375 3.177 80 552 2.573 .57 100 5200 17420 73 83 407 417 -50 789 684 105 1.975 679 null .506 null .982 null
17 1166 1615 770 730 396 885 1153 1564 778 734 383 834 0 0 211 293 93 70 93 100 84 100 1281 1217 .447 2.235 2.178 2.378 2.189 1.59 32 176 2.236 .8 60 1840 17650 98 104 73 79 0 1077 487 590 1.49 1043 556 .671 1.452 .575 .538
18 1109 1477 755 703 354 774 1119 1458 757 713 364 755 0 0 190 280 86 80 87 100 84 100 1128 1119 .457 2.186 2.074 2.407 2.37 1.739 32 176 2.104 .82 60 2060 17650 98 104 95 101 0 985 469 516 1.458 972 503 .686 1.383 .544 .468
19 778 800 725 701 53 99 738 709 731 701 13 8 0 0 222 422 92 78 21 18 8 10 152 21 .535 1.868 .615 .928 1.091 3.701 80 560 1.977 .66 100 2280 17640 95 105 115 125 -50 533 467 66 1.245 473 5 .803 .41 .316 -1.285
20 803 923 768 777 35 146 755 780 927 942 -13 3 0 0 256 542 1704 1297 1 5 0 2 181 -10 .24 4.171 null .854 .979 4.968 80 560 2.492 .69 100 2500 17640 95 105 137 147 -50 615 518 97 2.781 520 2 .36 null 1.476 null

Total number of rows: 7680

Table truncated, full table size 1798 Kbytes.




Supplementary data files not provided
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