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Sample GSM71867 Query DataSets for GSM71867
Status Public on Aug 26, 2005
Title 300p-19r 2C-N vs 2C-S
Sample type genomic
 
Channel 1
Source name 300p-19r 2C-S
Organism Helicobacter pylori
Characteristics 300p-19r 2C-S
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 300p-19r 2C-N
Organism Helicobacter pylori
Characteristics 300p-19r 2C-N
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Library Verification
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24535.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 Aug 25, 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 GPL15
Series (1)
GSE3197 MATT mapping of Transposon insertions sites of strain G27 GPS-cat library

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 1376 1207 216 1085 1160 122 1265 1144 220 1069 1049 59 0 0 440 252 33 237 100 37 100 12 1282 1108 9.508 .105 .056 .207 .238 2.495 32 176 .109 .23 60 1200 39810 93 99 110 116 0 2235 2009 226 .195 2119 109 5.134 .104 -2.36 -3.263
2 397 1073 220 1000 177 73 269 1081 223 1016 49 81 0 0 357 252 35 239 56 26 43 5 250 130 2.425 .412 1.653 1.872 2.109 6.137 80 552 2.118 .22 100 1420 39800 90 100 130 140 -100 1987 1852 135 .764 2002 150 1.309 3.061 -.389 1.614
3 1408 1219 247 1020 1161 199 1319 1156 252 1036 1072 136 0 0 580 331 35 258 100 33 100 8 1360 1208 5.834 .171 .127 .219 .31 2.794 12 104 .207 .25 50 1690 39800 92 97 159 164 0 2257 1889 369 .317 2141 252 3.15 .235 -1.656 -2.09
4 296 1077 261 995 35 82 263 1093 264 1017 2 98 0 0 140 260 41 238 20 26 11 6 117 100 .427 2.343 49 4.934 6.2 4.329 80 552 48.094 .06 100 1900 39800 90 100 178 188 -100 1994 1843 152 4.339 2024 181 .23 90.741 2.117 6.504
5 293 1065 275 1002 18 63 260 1043 285 1023 -15 41 0 0 128 327 121 361 10 8 7 1 81 26 .286 3.5 null 3.387 3.591 4.089 80 552 10.997 .3 100 2140 39800 90 100 202 212 -100 1972 1856 117 6.481 1931 76 .154 null 2.696 null
6 714 1077 294 1003 420 74 459 1041 298 1009 165 38 0 0 711 250 51 224 76 23 63 6 494 203 5.676 .176 .23 .764 .783 6.316 80 552 .153 .16 100 2380 39800 90 100 226 236 -100 1994 1857 137 .326 1928 70 3.065 .426 -1.616 -1.229
7 560 1332 293 983 267 349 344 979 338 1215 51 -4 0 0 547 2809 422 2443 21 2 11 1 616 47 .765 1.307 null 2.148 2.223 4.75 80 552 5.782 .98 100 2620 39800 90 100 250 260 -100 2467 1820 646 2.421 1813 null .413 null 1.275 null
8 417 951 286 968 131 -17 256 945 292 969 -30 -23 0 0 295 226 86 253 41 13 33 0 114 -53 null null null .981 1.342 4.602 80 552 12.911 .05 100 2860 39800 90 100 274 284 -100 1761 1793 -31 null 1750 null null null null null
9 20884 1357 344 1018 20540 339 20637 1325 422 1010 20293 307 0 0 4811 267 221 241 100 56 100 28 20879 20600 60.59 .017 .015 .021 .021 1.505 32 230 .017 .52 70 3090 39790 90 97 298 305 0 2513 1885 628 .031 2454 569 32.719 .028 -5.032 -5.158
10 499 1036 297 997 202 39 359 1007 304 1018 62 10 0 0 365 249 53 242 52 21 40 6 241 72 5.179 .193 .161 1.349 1.644 5.313 80 560 1.991 .19 100 3340 39800 90 100 322 332 -100 1919 1846 72 .358 1865 19 2.797 .299 -1.484 -1.743
11 545 1047 281 938 264 109 357 1033 298 1030 76 95 0 0 401 239 210 898 32 0 18 0 373 171 2.422 .413 1.25 .901 .94 4.709 80 552 5.405 .83 100 3570 39790 89 99 345 355 -100 1939 1737 202 .765 1913 176 1.308 2.315 -.387 1.211
12 1062 1276 268 995 794 281 1123 1272 269 1005 855 277 0 0 379 254 39 229 96 55 96 21 1075 1132 2.826 .354 .324 .429 .426 2.494 52 320 .376 .39 80 3820 39780 89 97 371 379 0 2363 1843 520 .655 2356 513 1.526 .6 -.61 -.737
13 2386 1349 250 978 2136 371 2516 1351 257 1004 2266 373 0 0 681 324 41 243 100 61 100 36 2507 2639 5.757 .174 .165 .169 .193 2.389 52 332 .149 .45 80 4060 39790 90 98 395 403 0 2498 1811 687 .322 2502 691 3.109 .305 -1.636 -1.714
14 535 1131 253 970 282 161 409 1102 253 964 156 132 0 0 281 289 44 268 71 26 57 11 443 288 1.752 .571 .846 .843 .756 5.276 80 552 2.888 .37 100 4290 39790 89 99 417 427 -50 2094 1796 298 1.057 2041 244 .946 1.567 .08 .648
15 636 982 112 524 524 458 560 969 171 630 448 445 0 0 478 358 99 383 72 60 61 18 982 893 1.144 .874 .993 1.46 1.334 3.507 80 552 1.549 .5 100 4530 39790 89 99 441 451 -50 1819 970 848 1.619 1794 824 .618 1.839 .695 .879
16 142 400 80 302 62 98 81 335 87 335 1 33 0 0 189 252 40 191 15 18 12 10 160 34 .633 1.581 33 4.496 4.818 3.101 80 552 2.1 .68 100 4770 39790 89 99 465 475 -100 741 559 181 2.927 620 61 .342 61.111 1.549 5.933
17 190 355 76 269 114 86 83 275 77 283 7 6 0 0 337 274 13 111 31 27 20 15 200 13 1.326 .754 .857 4.715 5.247 3.466 80 552 .919 .75 100 5010 39790 89 99 489 499 -100 657 498 159 1.397 509 11 .716 1.587 .482 .667
18 11946 2543 261 1047 11685 1496 11983 2584 288 1056 11722 1537 0 0 3621 651 103 247 100 96 100 93 13181 13259 7.811 .128 .131 .118 .119 1.528 32 170 .129 .92 60 1190 40030 115 121 109 115 0 4709 1939 2770 .237 4785 2846 4.218 .243 -2.077 -2.042
19 594 1083 256 1025 338 58 318 1108 259 1041 62 83 0 0 564 272 47 237 56 23 42 3 396 145 5.828 .172 1.339 1.271 1.061 5.919 80 560 .388 .26 100 1430 40040 114 124 131 141 -50 2006 1898 107 .318 2052 154 3.147 2.479 -1.654 1.31
20 415 1033 268 981 147 52 281 1004 271 990 13 23 0 0 383 223 43 222 33 25 26 2 199 36 2.827 .354 1.769 3.548 4.833 7.073 80 560 3.499 .07 100 1660 40040 114 124 154 164 -100 1913 1817 96 .655 1859 43 1.527 3.276 -.61 1.712

Total number of rows: 4608

Table truncated, full table size 1027 Kbytes.




Supplementary data files not provided
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