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Sample GSM184286 Query DataSets for GSM184286
Status Public on Aug 09, 2007
Title 259a4
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 259a4
Organism Helicobacter pylori
Characteristics 0.25 ug 259a4
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/2002-08/32372.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 8623 10720 286 176 8337 10544 6668 8123 291 183 6382 7947 0 0 6428 7722 58 64 100 100 98 100 18881 14329 .791 1.265 1.245 1.347 1.267 1.384 52 346 1.238 1 90 1790 12130 132 141 90 99 0 12762 210 12552 1.506 9670 9461 .664 1.482 .59 .568
2 5229 768 277 165 4952 603 2842 557 280 167 2565 392 0 0 5821 578 43 46 98 94 98 88 5555 2957 8.212 .122 .153 .143 .142 1.717 52 340 .102 .95 80 2040 12110 131 139 116 124 0 914 196 718 .145 663 467 6.898 .182 -2.786 -2.458
3 10538 9020 285 166 10253 8854 6853 5815 295 169 6568 5649 0 0 8333 7445 124 65 100 100 100 100 19107 12217 1.158 .864 .86 .836 .843 1.178 52 420 .876 1 90 2280 12110 130 139 139 148 0 10738 198 10540 1.028 6923 6725 .973 1.024 .04 .034
4 377 264 270 162 107 102 288 187 278 167 18 25 0 0 243 198 110 62 23 40 17 26 209 43 1.049 .953 1.389 1.248 1.122 3.257 80 560 .828 .81 100 2520 12110 130 140 163 173 0 314 193 121 1.135 223 30 .881 1.653 .182 .725
5 364 229 272 154 92 75 296 182 275 158 24 28 0 0 190 167 46 48 38 32 26 22 167 52 1.227 .815 1.167 .854 .886 3.007 80 560 .878 .78 100 2760 12100 129 139 187 197 0 273 183 89 .97 217 33 1.03 1.389 -.043 .474
6 12578 5042 300 174 12278 4868 8674 3029 305 181 8374 2855 0 0 11685 4857 62 54 100 100 100 100 17146 11229 2.522 .396 .341 .399 .39 1.288 52 420 .405 .99 90 3000 12110 130 139 211 220 0 6002 207 5795 .472 3606 3399 2.119 .406 -1.083 -1.301
7 472 351 300 171 172 180 334 220 304 174 34 49 0 0 370 353 49 56 38 45 25 27 352 83 .956 1.047 1.441 1.115 .998 3.395 80 552 .984 .93 100 3290 12080 127 137 240 250 0 418 204 214 1.246 262 58 .803 1.716 .317 .779
8 380 218 298 177 82 41 315 185 301 187 17 8 0 0 216 129 77 88 23 15 16 10 123 25 2 .5 .471 .714 .64 3.155 80 541 .617 .74 100 3530 12070 126 136 264 274 0 260 211 49 .595 220 10 1.68 .56 -.748 -.836
9 4269 4362 295 189 3974 4173 2169 2131 295 193 1874 1942 0 0 4132 4383 52 55 96 94 94 94 8147 3816 .952 1.05 1.036 1.04 1.048 1.172 52 416 1.055 1 90 3720 12100 129 138 283 292 0 5193 225 4968 1.25 2537 2312 .8 1.234 .322 .303
10 686 646 295 194 391 452 419 352 305 204 124 158 0 0 539 582 104 99 55 56 40 46 843 282 .865 1.156 1.274 1.105 1.303 2.664 80 560 1.098 .93 100 3950 12100 129 139 306 316 0 769 231 538 1.376 419 188 .727 1.517 .461 .601
11 561 490 291 198 270 292 361 323 295 204 70 125 0 0 374 340 51 56 53 71 45 52 562 195 .925 1.081 1.786 1.216 1.161 2.209 80 560 .95 .92 100 4200 12090 128 138 331 341 0 583 236 348 1.287 385 149 .777 2.126 .365 1.088
12 5498 4635 319 221 5179 4414 3762 3276 327 225 3443 3055 0 0 4319 3797 65 61 100 100 98 100 9593 6498 1.173 .852 .887 .846 .848 1.276 52 420 .864 .99 90 4440 12090 128 137 355 364 0 5518 263 5255 1.015 3900 3637 .986 1.056 .021 .079
13 1954 1201 343 205 1611 996 657 434 346 209 314 229 0 0 2558 1530 57 57 85 68 75 62 2607 543 1.617 .618 .729 .695 .67 2.469 80 560 .598 .98 100 4680 12090 128 138 379 389 0 1430 244 1186 .736 517 273 1.359 .868 -.442 -.204
14 11181 17965 376 264 10805 17701 11924 18377 385 283 11548 18113 0 0 4170 7178 86 131 100 100 100 100 28506 29661 .61 1.638 1.568 1.65 1.672 1.161 32 236 1.654 .99 70 4930 12090 129 136 405 412 0 21387 314 21073 1.95 21877 21563 .513 1.867 .964 .901
15 894 792 358 202 536 590 421 298 361 207 63 96 0 0 1090 1101 56 58 51 65 40 43 1126 159 .908 1.101 1.524 1.11 1.066 2.573 80 560 1.025 .98 100 5170 12080 127 137 428 438 0 943 240 702 1.31 355 114 .763 1.814 .39 .859
16 1699 1444 382 252 1317 1192 1275 1096 413 284 893 844 0 0 1367 1182 284 350 81 78 62 56 2509 1737 1.105 .905 .945 .87 .917 1.555 32 176 .88 .99 60 5400 12070 128 134 453 459 0 1719 300 1419 1.077 1305 1005 .928 1.125 .108 .17
17 2621 2106 391 266 2230 1840 1917 1637 402 266 1526 1371 0 0 1638 1380 67 74 100 100 100 100 4070 2897 1.212 .825 .898 .798 .883 1.264 32 236 .835 .98 70 5650 12080 128 135 477 484 0 2507 317 2190 .982 1949 1632 1.018 1.07 -.026 .097
18 2157 1461 271 170 1886 1291 1553 913 275 174 1282 743 0 0 2165 1580 48 50 98 96 92 90 3177 2025 1.461 .685 .58 .674 .648 1.55 52 320 .709 .98 80 1820 12360 156 164 94 102 0 1739 202 1537 .815 1087 885 1.227 .69 -.295 -.535
19 3916 3080 274 179 3642 2901 3420 2562 276 184 3146 2383 0 0 1700 1574 46 52 100 100 100 100 6543 5529 1.255 .797 .757 .781 .787 1.148 120 801 .822 .99 120 2060 12330 151 163 116 128 0 3667 213 3454 .948 3050 2837 1.055 .902 -.077 -.149
20 586 339 278 168 308 171 435 261 284 171 157 93 0 0 369 218 80 55 72 62 48 47 479 250 1.801 .555 .592 .516 .56 2.735 80 560 .564 .87 100 2300 12340 153 163 141 151 0 404 200 204 .661 311 111 1.513 .705 -.597 -.504

Total number of rows: 4608

Table truncated, full table size 1103 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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