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Sample GSM81867 Query DataSets for GSM81867
Status Public on Nov 04, 2005
Title sarb12 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 sarb12
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics sarb12
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22866.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 2928 1836 354 132 2574 1704 2049 1321 455 188 1695 1189 0 0 2087 1438 1272 845 69 59 34 32 4278 2884 1.511 .662 .701 .654 .664 1.232 52 412 .67 .98 90 880 18440 31 40 23 32 0 2961 213 2748 1.068 2131 1918 .937 1.131 .095 .178
2 3528 2213 387 152 3141 2061 1956 1175 447 188 1569 1023 0 0 3231 2181 1018 677 66 67 36 33 5202 2592 1.524 .656 .652 .649 .654 1.313 80 642 .662 .99 110 1110 18450 31 42 45 56 0 3569 245 3324 1.058 1895 1650 .945 1.052 .082 .073
3 1782 945 418 173 1364 772 937 502 430 180 519 329 0 0 1583 858 79 45 100 100 98 96 2136 848 1.767 .566 .634 .572 .557 1.54 52 340 .545 .98 80 1340 18440 32 40 70 78 0 1524 279 1245 .913 810 531 1.095 1.022 -.132 .032
4 4834 3074 468 200 4366 2874 3871 2172 512 231 3403 1972 0 0 3326 2232 300 183 100 100 97 98 7240 5375 1.519 .658 .579 .665 .68 1.275 80 638 .658 .99 110 1540 18430 29 40 88 99 0 4958 323 4635 1.062 3503 3181 .942 .935 .086 -.097
5 3637 2298 437 183 3200 2115 2464 1470 471 205 2027 1287 0 0 3329 2190 235 136 96 96 93 92 5315 3314 1.513 .661 .635 .672 .651 1.325 120 787 .657 .99 120 1790 18450 31 43 113 125 0 3706 295 3411 1.066 2371 2076 .938 1.024 .092 .034
6 3142 1894 400 155 2742 1739 2092 1104 402 160 1692 949 0 0 2411 1580 58 34 100 100 100 100 4481 2641 1.577 .634 .561 .64 .655 1.245 52 339 .641 .99 80 2010 18430 31 39 137 145 0 3055 250 2805 1.023 1781 1531 .978 .905 .033 -.145
7 3164 1945 444 166 2720 1779 1784 987 500 187 1340 821 0 0 2462 1619 556 154 92 100 53 96 4499 2161 1.529 .654 .613 .664 .665 1.289 52 420 .649 .98 90 2250 18430 30 39 160 169 0 3137 268 2869 1.055 1592 1324 .948 .988 .077 -.017
8 5707 3194 444 167 5263 3027 4525 2383 762 260 4081 2216 0 0 3496 2049 3264 1238 75 96 21 38 8290 6297 1.739 .575 .543 .573 .582 1.112 52 420 .329 .71 90 2480 18430 30 39 183 192 0 5152 269 4882 .928 3844 3574 1.078 .876 -.108 -.191
9 4892 2972 470 187 4422 2785 4267 2396 478 190 3797 2209 0 0 2927 1834 83 44 100 100 100 100 7207 6006 1.588 .63 .582 .644 .644 1.21 52 420 .623 .99 90 2690 18420 29 38 204 213 0 4794 302 4492 1.016 3865 3563 .984 .938 .023 -.092
10 3513 2455 477 195 3036 2260 2810 1882 481 197 2333 1687 0 0 2372 1746 72 41 100 100 100 100 5296 4020 1.343 .744 .723 .739 .756 1.368 80 552 .736 .99 100 2930 18420 29 39 228 238 0 3960 315 3645 1.201 3035 2721 .833 1.166 .264 .222
11 2129 1172 483 203 1646 969 1957 1148 500 210 1474 945 0 0 973 517 103 56 100 100 100 100 2615 2419 1.699 .589 .641 .611 .555 1.361 12 98 .512 .94 50 3140 18410 30 35 251 256 0 1890 327 1563 .95 1852 1524 1.053 1.034 -.075 .048
12 9424 5905 528 212 8896 5693 9431 5841 532 217 8903 5629 0 0 1598 1080 80 47 100 100 100 100 14589 14532 1.563 .64 .632 .639 .64 1.099 52 340 .637 .99 80 3380 18420 30 38 274 282 0 9524 342 9182 1.032 9421 9079 .969 1.02 .046 .028
13 1155 443 478 176 677 267 865 307 478 176 387 131 0 0 771 324 69 36 87 75 87 65 944 518 2.536 .394 .339 .304 .409 2.265 32 236 .383 .89 70 3610 18420 30 37 297 304 0 715 284 431 .636 495 211 1.572 .546 -.653 -.873
14 594 215 453 181 141 34 491 190 455 183 38 9 0 0 315 88 66 38 41 36 27 18 175 47 4.147 .241 .237 .345 .373 3.42 80 552 .222 .65 100 3830 18410 28 38 318 328 -50 347 292 55 .389 306 15 2.571 .382 -1.362 -1.388
15 1259 445 480 176 779 269 766 262 504 179 286 86 0 0 891 280 110 41 91 91 66 50 1048 372 2.896 .345 .301 .384 .257 1.901 12 98 .264 .83 50 4050 18400 29 34 342 347 0 718 284 434 .557 423 139 1.795 .485 -.844 -1.044
16 508 197 472 194 36 3 495 197 496 198 23 3 0 0 117 50 109 43 15 17 5 6 39 26 12 .083 .13 .447 .406 3.041 80 538 .201 .34 100 4280 18400 27 37 363 373 -50 318 313 5 .134 318 5 7.44 .21 -2.895 -2.249
17 845 329 380 142 465 187 610 168 384 148 230 26 0 0 700 454 60 59 94 34 82 23 652 256 2.487 .402 .113 .22 .321 3.003 52 340 .639 .86 80 900 18670 55 63 26 34 0 531 229 302 .649 271 42 1.542 .182 -.625 -2.455
18 664 254 404 156 260 98 505 181 407 158 101 25 0 0 460 239 60 35 65 43 45 25 358 126 2.653 .377 .248 .35 .339 3.16 80 554 .463 .88 100 1110 18660 53 63 46 56 -50 410 252 158 .608 292 40 1.645 .399 -.718 -1.325
19 499 178 428 167 71 11 458 173 430 172 30 6 0 0 184 55 65 38 31 16 15 11 82 36 6.455 .155 .2 .485 .466 3.591 80 560 .182 .46 100 1330 18650 52 62 68 78 -50 287 269 18 .25 279 10 4.002 .323 -2.001 -1.632
20 509 226 433 171 76 55 480 214 433 178 47 43 0 0 151 79 65 40 40 51 25 32 131 90 1.382 .724 .915 .732 .696 2.607 80 560 .399 .59 100 1560 18650 52 62 91 101 -50 365 276 89 1.167 345 69 .857 1.476 .223 .561

Total number of rows: 7680

Table truncated, full table size 1770 Kbytes.




Supplementary data files not provided
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