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Sample GSM81856 Query DataSets for GSM81856
Status Public on Nov 04, 2005
Title SARA53 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 SARA53
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics SARA53
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26440.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 2731 5221 339 1605 2392 3616 1460 3182 358 1712 1121 1577 0 0 3219 5369 121 586 88 80 78 60 6008 2698 .662 1.512 1.407 1.711 1.561 2.633 120 767 1.662 .96 120 1210 19020 76 88 39 51 0 8158 2508 5650 2.362 4972 2464 .423 2.198 1.24 1.136
2 7861 8076 355 1533 7506 6543 4788 4451 367 1607 4433 2918 0 0 6655 7505 92 471 100 97 100 92 14049 7351 1.147 .872 .658 .703 .717 1.626 80 547 1.017 .96 100 1420 19040 79 89 61 71 0 12619 2395 10223 1.362 6955 4559 .734 1.029 .446 .041
3 7148 5778 508 1893 6640 3885 7090 5600 568 1914 6582 3707 0 0 2112 1065 265 566 100 100 100 100 10525 10289 1.709 .585 .563 .593 .596 1.185 12 104 .615 .92 50 1650 19020 79 84 86 91 0 9028 2958 6070 .914 8750 5792 1.094 .88 -.129 -.184
4 10522 12470 393 1635 10129 10835 6864 6754 429 1698 6471 5119 0 0 8309 11279 178 493 100 100 100 96 20964 11590 .935 1.07 .791 .899 .929 1.534 80 656 1.222 .97 110 1880 19020 76 87 106 117 0 19484 2555 16930 1.671 10553 7998 .598 1.236 .741 .306
5 10549 7401 339 1261 10210 6140 8141 5705 376 1304 7802 4444 0 0 6847 4987 179 339 100 100 100 100 16350 12246 1.663 .601 .57 .526 .557 1.397 52 420 .657 .97 90 2100 19010 76 85 129 138 0 11564 1970 9594 .94 8914 6944 1.064 .89 -.09 -.168
6 6364 4614 341 1387 6023 3227 5448 4257 398 1504 5107 2870 0 0 3076 1657 241 1226 100 92 100 63 9250 7977 1.866 .536 .562 .525 .531 1.329 52 332 .643 .72 80 2330 19010 77 85 153 161 0 7209 2167 5042 .837 6652 4484 1.195 .878 -.256 -.188
7 5327 4381 344 1421 4983 2960 5582 4112 408 1447 5238 2691 0 0 2189 1507 246 374 100 100 100 96 7943 7929 1.683 .594 .514 .577 .576 1.392 32 236 .613 .93 70 2550 19010 77 84 175 182 0 6845 2220 4625 .928 6425 4205 1.077 .803 -.108 -.317
8 11783 7837 341 1516 11442 6321 10114 6848 341 1544 9773 5332 0 0 5418 3220 60 373 100 100 100 100 17763 15105 1.81 .552 .546 .541 .554 1.23 52 332 .558 .97 80 2780 19010 77 85 198 206 0 12245 2369 9877 .863 10700 8331 1.159 .852 -.212 -.23
9 12356 8499 356 1528 12000 6971 11549 7706 357 1535 11193 6178 0 0 6639 4365 59 331 100 98 100 98 18971 17371 1.721 .581 .552 .534 .591 1.491 52 420 .606 .97 90 3010 19000 75 84 220 229 0 13280 2388 10892 .908 12041 9653 1.102 .862 -.14 -.214
10 8654 5868 350 1383 8304 4485 7627 5356 365 1437 7277 3973 0 0 4295 2288 135 612 100 100 100 98 12789 11250 1.852 .54 .546 .549 .531 1.349 52 420 .527 .96 90 3230 19000 75 84 242 251 0 9169 2161 7008 .844 8369 6208 1.185 .853 -.245 -.229
11 2422 2565 361 1280 2061 1285 2140 2351 372 1328 1779 1071 0 0 950 705 96 328 100 100 100 78 3346 2850 1.604 .623 .602 .592 .628 1.545 32 236 .649 .84 70 3450 19000 76 83 265 272 0 4008 2000 2008 .974 3673 1673 1.026 .941 -.038 -.088
12 14420 10769 346 1405 14074 9364 14700 11195 350 1441 14354 9790 0 0 2946 2760 52 347 100 100 100 100 23438 24144 1.503 .665 .682 .641 .676 1.266 52 412 .696 .97 90 3690 18990 74 83 288 297 0 16827 2195 14631 1.04 17492 15297 .962 1.066 .056 .092
13 2652 3680 332 1265 2320 2415 1904 3431 337 1278 1572 2166 0 0 1931 1265 56 308 100 98 98 96 4735 3738 .961 1.041 1.378 1.409 1.349 2.168 52 332 .871 .88 80 3920 18990 75 83 312 320 0 5750 1977 3773 1.626 5361 3384 .615 2.153 .702 1.106
14 927 2322 326 1400 601 922 763 2217 338 1449 437 817 0 0 411 486 55 363 100 91 100 75 1523 1254 .652 1.534 1.87 1.66 1.96 2.048 12 104 3.014 .45 50 4140 18990 76 81 335 340 0 3628 2188 1441 2.397 3464 1277 .417 2.921 1.261 1.547
15 647 2671 311 1305 336 1366 552 2520 320 1386 241 1215 0 0 370 1049 71 412 86 84 69 63 1702 1456 .246 4.065 5.041 4.316 4.77 3.099 52 340 6.837 .47 80 4360 19000 76 84 356 364 0 4173 2039 2134 6.352 3938 1898 .157 7.877 2.667 2.978
16 566 1479 308 1475 258 4 518 1389 312 1534 210 -86 0 0 265 340 58 528 73 7 63 1 262 124 64.5 .016 null 1.41 1.255 4.055 52 412 -1 -1 90 4580 18980 73 82 377 386 -50 2311 2305 6 .024 2170 null 41.28 null -5.367 null
17 654 3090 309 1428 345 1662 565 2975 313 1457 256 1547 0 0 359 987 58 395 78 94 69 80 2007 1803 .208 4.817 6.043 6.169 5.984 2.454 52 332 4.996 .7 80 1210 19260 102 110 41 49 0 4828 2231 2597 7.527 4648 2417 .133 9.442 2.912 3.239
18 729 2831 353 1493 376 1338 639 2746 356 1510 286 1253 0 0 341 776 61 373 93 90 78 78 1714 1539 .281 3.559 4.381 4.704 4.669 2.252 32 236 4.779 .61 70 1430 19240 100 107 63 70 0 4423 2333 2091 5.56 4291 1958 .18 6.845 2.475 2.775
19 503 1533 356 1415 147 118 440 1439 360 1456 84 24 0 0 195 388 67 360 55 23 38 7 265 108 1.246 .803 .286 2.099 2.269 5.233 52 420 9.462 .27 90 1650 19240 99 108 84 93 -50 2395 2211 184 1.254 2248 38 .797 .446 .327 -1.163
20 663 1580 376 1400 287 180 605 1551 385 1455 229 151 0 0 212 334 75 396 86 26 73 3 467 380 1.594 .627 .659 .904 .932 2.723 52 420 7.31 .3 90 1880 19240 99 108 107 116 -50 2469 2188 281 .98 2423 236 1.02 1.03 -.029 .043

Total number of rows: 7680

Table truncated, full table size 1821 Kbytes.




Supplementary data files not provided
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