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Sample GSM184321 Query DataSets for GSM184321
Status Public on Aug 09, 2007
Title 259i9
Sample type genomic
 
Channel 1
Source name 0.25 ug Tigr/Astra Reference
Organism Helicobacter pylori
Characteristics 0.25 ug Tigr/Astra Reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.25 ug 259i9
Organism Helicobacter pylori
Characteristics 0.25 ug 259i9
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32383.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 Apr 25, 2007
Last update date Aug 08, 2007
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)
GSE7618 Array CGH of Mexican Patient Isolates and BCS100 Strain

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 6890 8061 231 194 6659 7867 5728 6526 251 208 5497 6332 0 0 3493 4075 120 93 100 100 100 100 14526 11829 .846 1.181 1.152 1.181 1.209 1.177 52 420 1.181 .98 90 1160 40600 103 112 80 89 0 8668 209 8459 1.27 7017 6809 .787 1.239 .345 .309
2 2995 628 215 167 2780 461 2501 502 219 170 2286 335 0 0 1594 564 47 42 100 96 100 92 3241 2621 6.03 .166 .147 .139 .132 1.871 52 420 .155 .55 90 1390 40590 102 111 103 112 0 675 180 496 .178 540 360 5.608 .158 -2.488 -2.666
3 6729 5895 212 167 6517 5728 5659 4803 215 173 5447 4636 0 0 4434 3802 49 47 100 100 100 100 12245 10083 1.138 .879 .851 .919 .832 1.74 52 420 .868 .97 90 1630 40590 102 111 127 136 0 6339 180 6159 .945 5165 4985 1.058 .915 -.081 -.128
4 309 270 210 163 99 107 246 215 242 277 36 52 0 0 256 278 541 1878 3 1 2 0 206 88 .925 1.081 1.444 1.38 1.322 4.193 80 560 3.617 .96 100 1870 40580 101 111 151 161 0 290 175 115 1.162 231 56 .86 1.553 .217 .635
5 292 252 204 166 88 86 226 184 212 170 22 18 0 0 195 270 53 50 36 36 28 28 174 40 1.023 .977 .818 .822 .919 2.92 52 340 .839 .61 80 2130 40580 102 110 178 186 0 271 178 92 1.051 198 19 .952 .88 .072 -.185
6 7173 3731 216 167 6957 3564 5022 2453 232 176 4806 2286 0 0 5607 3160 74 56 100 100 100 100 10521 7092 1.952 .512 .476 .452 .485 1.493 52 340 .528 .96 80 2370 40580 102 110 202 210 0 4012 180 3832 .551 2638 2458 1.815 .511 -.86 -.967
7 588 629 200 169 388 460 435 395 206 170 235 226 0 0 559 792 66 41 75 90 67 80 848 461 .843 1.186 .962 1.32 1.177 2.123 52 340 1.507 .72 80 2610 40580 102 110 226 234 0 676 182 495 1.275 425 243 .784 1.034 .35 .048
8 393 346 204 175 189 171 310 224 214 185 106 49 0 0 338 382 63 64 65 40 46 28 360 155 1.105 .905 .462 .613 .691 2.849 52 340 1.086 .86 80 2850 40580 102 110 250 258 0 372 188 184 .973 241 53 1.028 .497 -.04 -1.009
9 2804 3178 194 164 2610 3014 2108 2395 203 178 1914 2231 0 0 1850 2156 103 95 100 100 100 100 5624 4145 .866 1.155 1.166 1.117 1.174 1.442 52 340 1.166 .95 80 3090 40580 102 110 274 282 0 3417 176 3241 1.242 2575 2399 .805 1.253 .312 .326
10 676 791 189 162 487 629 491 575 195 166 302 413 0 0 498 666 57 46 90 92 76 88 1116 715 .774 1.292 1.368 1.488 1.419 2.151 52 332 1.289 .81 80 3320 40570 101 109 297 305 0 851 174 676 1.389 618 444 .72 1.47 .474 .556
11 457 481 184 158 273 323 400 406 186 164 216 248 0 0 279 411 33 41 82 88 75 75 596 464 .845 1.183 1.148 1.213 1.282 2.677 52 332 1.8 .78 80 3560 40570 101 109 321 329 0 517 170 347 1.272 437 267 .786 1.235 .347 .304
12 2365 4332 194 173 2171 4159 2399 3990 198 178 2205 3817 0 0 1275 2780 50 53 100 100 100 100 6330 6022 .522 1.916 1.731 1.728 1.769 1.457 52 332 2.065 .95 80 3800 40570 101 109 345 353 0 4658 186 4472 2.06 4290 4104 .485 1.861 1.043 .896
13 1397 1857 195 165 1202 1692 982 1475 203 176 787 1310 0 0 1059 1419 48 59 92 96 82 88 2894 2097 .71 1.408 1.665 1.551 1.456 1.52 52 332 1.392 .95 80 4040 40570 101 109 369 377 0 1997 177 1819 1.514 1586 1409 .661 1.79 .598 .84
14 5177 8045 196 160 4981 7885 6553 10487 211 185 6357 10327 0 0 3394 5404 71 92 92 100 90 94 12866 16684 .632 1.583 1.625 1.692 1.584 1.659 52 332 1.615 .97 80 4280 40570 101 109 393 401 0 8651 172 8478 1.702 11276 11104 .587 1.747 .767 .805
15 701 465 198 157 503 308 373 280 200 162 175 123 0 0 638 397 36 48 82 65 65 53 811 298 1.633 .612 .703 .632 .721 2.094 52 332 .599 .83 80 4520 40570 101 109 417 425 0 500 169 331 .658 301 132 1.519 .756 -.603 -.404
16 745 729 207 160 538 569 634 505 214 167 427 345 0 0 517 625 72 52 88 88 78 75 1107 772 .946 1.058 .808 .861 .99 2.355 52 332 1.146 .92 80 4760 40570 101 109 441 449 0 784 172 612 1.137 543 371 .879 .869 .186 -.203
17 1562 1745 194 158 1368 1587 1343 1431 197 162 1149 1273 0 0 1086 1266 37 45 96 98 96 96 2955 2422 .862 1.16 1.108 1.207 1.226 1.634 52 324 1.171 .93 80 5000 40570 101 109 465 473 0 1876 170 1706 1.247 1539 1369 .802 1.191 .319 .253
18 1023 761 285 259 738 502 569 405 313 289 284 146 0 0 1229 936 139 181 70 45 51 25 1240 430 1.47 .68 .514 .635 .613 2.205 80 560 .726 .91 100 1170 40820 125 135 81 91 0 818 278 540 .731 435 157 1.367 .553 -.451 -.855
19 4039 6039 294 272 3745 5767 3878 5390 462 458 3584 5118 0 0 808 1984 455 522 100 100 100 100 9512 8702 .649 1.54 1.428 1.49 1.434 1.211 52 420 1.64 .96 90 1380 40810 124 133 102 111 0 6494 292 6201 1.656 5796 5503 .604 1.535 .728 .619
20 444 357 214 179 230 178 362 263 256 217 148 84 0 0 246 242 133 126 52 41 36 27 408 232 1.292 .774 .568 .731 .744 2.288 80 560 .904 .78 100 1650 40820 125 135 129 139 0 384 192 191 .832 283 90 1.202 .61 -.265 -.712

Total number of rows: 4608

Table truncated, full table size 1075 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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