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Sample GSM81885 Query DataSets for GSM81885
Status Public on Nov 04, 2005
Title TY2 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 TY2
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics TY2
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22854.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 1100 2109 190 426 910 1683 995 2017 192 432 805 1591 0 0 517 782 27 75 100 100 100 100 2593 2396 .541 1.849 1.976 1.924 1.981 1.237 32 220 1.772 .97 70 1620 17310 75 82 50 57 0 1562 316 1247 1.37 1494 1179 .73 1.464 .454 .55
2 1498 2672 194 444 1304 2228 1204 2225 197 450 1010 1781 0 0 1021 1530 34 83 100 100 100 100 3532 2791 .585 1.709 1.763 1.882 1.754 1.299 52 340 1.615 .99 80 1860 17310 75 83 74 82 0 1979 329 1650 1.266 1648 1319 .79 1.306 .34 .385
3 682 1148 185 403 497 745 499 968 183 412 314 565 0 0 417 550 23 78 100 100 100 100 1242 879 .667 1.499 1.799 1.619 1.613 1.307 32 170 1.403 .97 60 2070 17300 75 81 96 102 0 850 299 552 1.11 717 419 .901 1.333 .151 .415
4 1970 3532 217 482 1753 3050 1166 2252 225 491 949 1770 0 0 1598 2567 49 102 100 100 97 100 4803 2719 .575 1.74 1.865 1.979 1.758 1.51 80 552 1.673 .99 100 2310 17300 73 83 118 128 0 2616 357 2259 1.289 1668 1311 .776 1.382 .366 .466
5 2431 4319 254 519 2177 3800 2030 4044 254 529 1776 3525 0 0 1551 2325 40 93 100 100 100 100 5977 5301 .573 1.746 1.985 1.969 1.8 1.455 52 412 1.659 .98 90 2520 17290 72 81 139 148 0 3199 384 2815 1.293 2996 2611 .773 1.47 .371 .556
6 1413 2472 233 491 1180 1981 897 1719 236 495 664 1228 0 0 1015 1602 38 89 100 100 100 100 3161 1892 .596 1.679 1.849 1.726 1.721 1.221 52 340 1.643 .98 80 2760 17300 74 82 164 172 0 1831 364 1467 1.244 1273 910 .804 1.37 .314 .454
7 1156 2072 229 508 927 1564 666 1417 228 509 437 909 0 0 1011 1508 30 85 100 100 100 98 2491 1346 .593 1.687 2.08 1.85 1.798 1.336 52 340 1.581 .98 80 2990 17300 74 82 187 195 0 1535 376 1159 1.25 1050 673 .8 1.541 .322 .624
8 1768 2916 216 501 1552 2415 1343 2258 219 505 1127 1757 0 0 1099 1782 32 90 100 100 100 100 3967 2884 .643 1.556 1.559 1.5 1.54 1.227 52 340 1.587 .98 80 3210 17300 74 82 209 217 0 2160 371 1789 1.153 1673 1301 .868 1.155 .205 .208
9 2038 3711 221 481 1817 3230 1361 2553 224 487 1140 2072 0 0 1651 2593 34 86 96 100 92 97 5047 3212 .563 1.778 1.818 2.074 1.787 1.759 80 552 1.677 .99 100 3430 17290 72 82 230 240 0 2749 356 2393 1.317 1891 1535 .759 1.346 .397 .429
10 2068 3880 221 453 1847 3427 1727 3549 226 461 1506 3096 0 0 1031 1679 37 79 100 100 100 100 5274 4602 .539 1.855 2.056 1.905 1.87 1.144 52 420 1.799 .99 90 3660 17290 72 81 253 262 0 2874 336 2539 1.374 2629 2293 .728 1.523 .459 .607
11 826 1337 232 481 594 856 762 1373 235 502 530 892 0 0 351 243 44 108 100 100 100 100 1450 1422 .694 1.441 1.683 1.623 1.638 1.456 12 104 1.28 .85 50 3880 17300 75 80 277 282 0 990 356 634 1.067 1017 661 .937 1.247 .094 .318
12 3775 2146 239 518 3536 1628 3787 2055 242 522 3548 1537 0 0 1045 550 40 95 100 100 100 100 5164 5085 2.172 .46 .433 .461 .452 1.281 52 332 .452 .96 80 4110 17280 72 80 299 307 0 1590 384 1206 .341 1522 1139 2.932 .321 -1.552 -1.64
13 451 1346 247 505 204 841 349 1081 251 519 102 576 0 0 233 540 39 102 71 100 56 100 1045 678 .243 4.123 5.647 5.491 5.206 2.141 32 236 3.542 .85 70 4330 17300 74 81 321 328 0 997 374 623 3.054 801 427 .327 4.183 1.611 2.065
14 280 699 236 518 44 181 265 572 239 533 29 54 0 0 87 346 34 89 43 45 21 28 225 83 .243 4.114 1.862 3.159 3.938 3.321 80 552 5.882 .58 100 4540 17280 71 81 341 351 -50 518 384 134 3.047 424 40 .328 1.379 1.607 .464
15 356 1710 235 540 121 1170 355 1805 237 553 120 1265 0 0 83 355 29 93 83 100 66 100 1291 1385 .103 9.669 10.542 10.875 8.819 1.847 12 104 11.225 .64 50 4770 17290 74 79 366 371 0 1267 400 867 7.163 1337 937 .14 7.809 2.84 2.965
16 260 622 240 513 20 109 246 577 242 518 6 64 0 0 57 165 35 90 26 43 15 25 129 70 .183 5.45 10.667 3.014 3.019 3.946 80 538 8.582 .31 100 4990 17270 70 80 386 396 -50 461 380 81 4.037 427 47 .248 7.901 2.013 2.982
17 535 2684 206 430 329 2254 298 1877 208 435 92 1447 0 0 866 3810 32 71 75 100 56 96 2583 1539 .146 6.851 15.728 10.673 11.574 2.053 32 176 4.779 .97 60 1640 17530 98 104 53 59 0 1988 319 1670 5.075 1390 1072 .197 11.651 2.343 3.542
18 313 1860 214 467 99 1393 300 1828 216 471 86 1361 0 0 86 419 27 91 75 100 58 100 1492 1447 .071 14.071 15.826 17.175 11.881 2.261 12 104 14.738 .74 50 1850 17530 98 103 74 79 0 1378 346 1032 10.423 1354 1008 .096 11.723 3.382 3.551
19 214 444 212 438 2 6 203 437 215 445 -9 -1 0 0 49 93 31 80 18 22 7 5 8 -10 .333 3 null 2.002 1.942 3.409 80 560 14.095 .14 100 2080 17520 95 105 95 105 -50 329 324 4 2.222 324 null .45 null 1.152 null
20 237 496 220 468 17 28 221 447 224 477 1 -21 0 0 74 167 40 96 18 15 11 13 45 -20 .607 1.647 null 2.631 2.865 4.388 80 560 4.191 .52 100 2300 17520 95 105 117 127 -50 367 347 21 1.22 331 null .82 null .287 null

Total number of rows: 7680

Table truncated, full table size 1768 Kbytes.




Supplementary data files not provided
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