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Sample GSM81877 Query DataSets for GSM81877
Status Public on Nov 04, 2005
Title sarb64 v SL1344 3
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 sarb64
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Characteristics sarb64
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22613.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
1 478 529 105 141 373 388 331 348 107 142 226 207 0 0 314 361 21 27 100 100 100 100 761 433 .961 1.04 .916 .985 1.016 1.233 52 332 1.104 .98 80 2190 18210 45 53 67 75 0 705 188 517 1.387 464 276 .721 1.221 .472 .288
2 1350 1350 152 188 1198 1162 1278 1289 175 204 1126 1101 0 0 523 501 90 85 100 100 100 100 2360 2227 1.031 .97 .978 .973 .936 1.188 32 236 .985 .98 70 2410 18190 43 50 89 96 0 1800 251 1549 1.293 1719 1468 .773 1.304 .371 .383
3 283 323 179 222 104 101 208 242 178 222 29 20 0 0 195 207 29 38 50 43 40 31 205 49 1.03 .971 .69 1.046 1.046 2.927 80 552 1.074 .94 100 2630 18190 42 52 110 120 -50 431 296 135 1.295 323 27 .772 .92 .373 -.121
4 1222 1341 198 244 1024 1097 984 1161 199 246 786 917 0 0 716 758 31 42 97 98 97 96 2121 1703 .933 1.071 1.167 1.043 1.041 1.498 80 644 1.076 .98 110 2870 18200 42 53 133 144 0 1788 325 1463 1.428 1548 1223 .7 1.556 .514 .637
5 1059 1023 202 247 857 776 941 947 203 247 739 700 0 0 612 559 32 40 98 97 98 91 1633 1439 1.104 .905 .947 .835 .855 1.362 80 560 .919 .98 100 3090 18200 43 53 156 166 0 1364 329 1035 1.207 1263 933 .828 1.263 .272 .337
6 813 954 168 212 645 742 546 617 173 215 378 405 0 0 633 749 37 45 88 86 86 86 1387 783 .869 1.15 1.071 1.118 1.122 1.36 52 340 1.176 .99 80 3300 18210 45 53 178 186 0 1272 283 989 1.534 823 540 .652 1.429 .617 .515
7 655 745 151 195 504 550 368 407 151 196 217 212 0 0 545 630 19 27 100 100 100 96 1054 429 .916 1.091 .977 1.006 1.042 1.501 52 420 1.133 .98 90 3540 18200 43 52 201 210 0 993 260 733 1.455 543 283 .687 1.303 .541 .381
8 997 826 153 190 844 636 706 607 153 192 553 417 0 0 757 610 19 28 100 98 100 97 1480 970 1.327 .754 .754 .7 .739 1.417 80 554 .78 .98 100 3760 18200 43 53 223 233 0 1101 253 848 1.005 809 556 .995 1.005 .007 .008
9 1323 1322 156 191 1167 1131 1164 1151 158 192 1008 960 0 0 726 792 21 27 100 100 100 100 2298 1968 1.032 .969 .952 .928 .936 1.294 80 554 1.024 .97 100 3990 18200 43 53 246 256 0 1763 255 1508 1.292 1535 1280 .774 1.27 .37 .345
10 780 753 160 197 620 556 676 647 161 199 516 450 0 0 474 446 22 29 98 92 96 88 1176 966 1.115 .897 .872 .821 .89 1.567 80 555 .922 .98 100 4210 18200 43 53 268 278 0 1004 263 741 1.196 863 600 .836 1.163 .258 .218
11 243 271 151 189 92 82 182 207 150 191 31 18 0 0 172 177 24 32 57 36 32 25 174 49 1.122 .891 .581 .958 .987 2.354 80 533 1.02 .94 100 4420 18180 41 51 289 299 -50 361 252 109 1.188 276 24 .841 .774 .249 -.369
12 1782 782 156 181 1626 601 1797 751 158 183 1641 570 0 0 306 239 22 28 100 100 100 100 2227 2211 2.705 .37 .347 .344 .356 1.347 52 420 .38 .95 90 4660 18200 43 52 313 322 0 1043 241 801 .493 1001 760 2.029 .463 -1.021 -1.111
13 201 197 141 177 60 20 169 178 144 177 28 1 0 0 94 62 22 26 58 28 32 17 80 29 3 .333 .036 .89 .767 4.123 80 538 .598 .69 100 4870 18180 41 51 334 344 -50 263 236 27 .444 237 1 2.25 .048 -1.17 -4.392
14 142 179 134 171 8 8 136 177 134 172 2 6 0 0 42 40 16 26 23 16 8 5 16 8 1 1 3 1.57 1.659 3.243 80 538 1.244 .49 100 5090 18180 41 51 356 366 -50 239 228 11 1.333 236 8 .75 4 .415 2
15 149 170 134 173 15 -3 135 165 135 174 1 -8 0 0 44 41 16 26 26 17 15 10 12 -7 null null null 1.726 1.652 4.354 80 538 1.309 .42 100 5320 18180 41 51 379 389 -50 227 231 -4 null 220 null null null null null
16 148 191 135 175 13 16 141 190 136 177 6 15 0 0 38 34 17 26 28 33 12 7 29 21 .813 1.231 2.5 1.306 1.455 4.147 80 538 1.747 .3 100 5540 18180 41 51 401 411 -50 255 233 21 1.641 253 20 .609 3.333 .715 1.737
17 120 147 103 141 17 6 108 137 105 143 5 -4 0 0 43 30 19 26 23 22 11 8 23 1 2.833 .353 null 1.739 1.412 4.193 80 552 .735 .32 100 2190 18420 65 75 66 76 -50 196 188 8 .471 183 null 2.125 null -1.087 null
18 137 164 132 169 5 -5 128 162 133 171 -4 -7 0 0 42 37 20 27 22 20 13 6 0 -11 null null null 1.109 1.286 4.011 80 560 1.186 .46 100 2410 18420 65 75 88 98 -50 219 225 -7 null 216 null null null null null
19 142 168 145 178 -3 -10 143 165 148 182 -2 -13 0 0 29 39 27 35 15 15 1 1 -13 -15 null null null 1.319 1.374 2.847 80 560 1.609 .6 100 2630 18420 65 75 110 120 -50 224 237 -13 null 220 null null null null null
20 151 171 157 195 -6 -24 148 176 164 194 -9 -19 0 0 33 40 117 44 0 3 0 0 -30 -28 null null null 1.362 1.245 2.92 80 560 1.53 .58 100 2860 18420 65 75 133 143 -50 228 260 -32 null 235 null null null null null

Total number of rows: 7680

Table truncated, full table size 1696 Kbytes.




Supplementary data files not provided
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