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Sample GSM184288 Query DataSets for GSM184288
Status Public on Aug 09, 2007
Title 259c8
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 259c8
Organism Helicobacter pylori
Characteristics 0.25 ug 259c8
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/2002-08/32373.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 9376 10645 293 242 9083 10403 7438 8004 299 254 7145 7762 0 0 6390 7370 68 79 98 100 98 100 19486 14907 .873 1.145 1.086 1.258 1.139 1.817 52 420 1.144 .99 90 2000 40050 122 131 133 142 0 10645 242 10403 1.145 8004 7762 .873 1.086 .196 .119
2 7154 1651 298 234 6856 1417 5801 1156 315 243 5503 922 0 0 4465 1294 101 71 100 100 100 96 8273 6425 4.838 .207 .168 .16 .159 1.81 32 230 .197 .82 70 2240 40040 122 129 158 165 0 1651 234 1417 .207 1156 922 4.838 .168 -2.275 -2.577
3 12338 10780 301 269 12037 10511 12173 10407 316 305 11872 10138 0 0 7812 6737 89 155 100 100 98 98 22548 22010 1.145 .873 .854 .904 .876 1.216 52 384 .869 1 90 2480 40020 119 128 181 190 0 10780 269 10511 .873 10407 10138 1.145 .854 -.196 -.228
4 527 564 301 254 226 310 322 284 459 530 21 30 0 0 752 1204 996 1444 5 5 1 1 536 51 .729 1.372 1.429 1.33 1.318 2.829 80 560 1.17 .95 100 2710 40050 122 132 204 214 0 564 254 310 1.372 284 30 .729 1.429 .456 .515
5 1763 2162 298 256 1465 1906 344 346 356 340 46 90 0 1 7643 8705 455 536 17 26 7 15 3371 136 .769 1.301 1.957 1.345 1.533 3.932 80 560 1.159 .97 100 2950 40050 122 132 228 238 0 2162 256 1906 1.301 346 90 .769 1.957 .38 .968
6 8234 4161 296 253 7938 3908 3248 1880 337 342 2952 1627 0 0 9804 4651 391 1298 91 57 78 38 11846 4579 2.031 .492 .551 .56 .506 1.724 80 538 .768 .87 100 3200 40030 120 130 253 263 0 4161 253 3908 .492 1880 1627 2.031 .551 -1.022 -.859
7 689 753 277 219 412 534 331 325 283 229 54 106 0 0 800 1039 50 58 51 57 45 45 946 160 .772 1.296 1.963 1.222 1.249 2.904 80 522 1.306 .97 100 3440 40020 119 129 277 287 0 753 219 534 1.296 325 106 .772 1.963 .374 .973
8 413 315 282 227 131 88 326 235 288 230 44 8 0 0 222 237 52 59 46 35 37 26 219 52 1.489 .672 .182 .737 .751 3.726 80 522 1.184 .67 100 3680 40020 119 129 301 311 0 315 227 88 .672 235 8 1.489 .182 -.574 -2.459
9 5752 6746 299 251 5453 6495 4384 6061 310 263 4085 5810 0 0 4146 5106 68 81 100 100 100 100 11948 9895 .84 1.191 1.422 1.217 1.231 1.221 32 220 1.212 .99 70 3930 40030 121 128 327 334 0 6746 251 6495 1.191 6061 5810 .84 1.422 .252 .508
10 688 725 291 240 397 485 426 428 295 243 135 188 0 0 567 655 51 59 70 68 60 58 882 323 .819 1.222 1.393 1.239 1.227 2.08 80 522 1.168 .97 100 4160 40020 119 129 349 359 0 725 240 485 1.222 428 188 .819 1.393 .289 .478
11 548 569 297 249 251 320 345 354 303 255 48 105 0 0 381 524 54 70 48 56 40 42 571 153 .784 1.275 2.188 1.083 1.11 3.321 80 480 1.371 .93 100 4400 40000 117 127 373 383 0 569 249 320 1.275 354 105 .784 2.188 .35 1.129
12 3749 5397 322 273 3427 5124 3307 4468 338 289 2985 4195 0 0 2784 4148 163 153 96 100 86 96 8551 7180 .669 1.495 1.405 1.589 1.532 1.319 52 366 1.497 .99 90 4620 40010 118 127 395 404 0 5397 273 5124 1.495 4468 4195 .669 1.405 .58 .491
13 2923 3991 326 274 2597 3717 2774 4073 336 287 2448 3799 0 0 1797 2488 71 97 100 100 100 100 6314 6247 .699 1.431 1.552 1.438 1.422 1.186 32 174 1.419 .99 70 4870 40000 118 125 421 428 0 3991 274 3717 1.431 4073 3799 .699 1.552 .517 .634
14 6595 10997 344 302 6251 10695 6916 9814 342 304 6572 9512 0 0 4811 7827 62 72 96 100 92 100 16946 16084 .584 1.711 1.447 2.07 1.745 1.575 52 270 1.68 .99 80 5110 40000 118 126 445 453 0 10997 302 10695 1.711 9814 9512 .584 1.447 .775 .533
15 1099 961 329 282 770 679 417 377 346 291 88 95 0 0 1854 1614 150 87 40 50 33 41 1449 183 1.134 .882 1.08 1.267 .935 3.004 80 480 .856 .94 100 5360 40000 117 127 469 479 0 961 282 679 .882 377 95 1.134 1.08 -.181 .11
16 1849 2007 296 239 1553 1768 1683 1844 302 250 1387 1605 0 0 1183 1173 59 92 100 100 100 100 3321 2992 .878 1.138 1.157 1.261 1.273 1.49 12 64 1.052 .94 50 5600 40000 119 124 495 500 0 2007 239 1768 1.138 1844 1605 .878 1.157 .187 .211
17 1828 2846 329 292 1499 2554 1246 1733 335 306 917 1441 0 0 1457 2458 68 90 100 100 100 100 4053 2358 .587 1.704 1.571 1.612 1.712 1.343 32 190 1.686 .98 70 5830 40010 119 126 517 524 0 2846 292 2554 1.704 1733 1441 .587 1.571 .769 .652
18 3101 2169 304 253 2797 1916 1303 1029 319 265 999 776 0 0 3386 2193 94 101 100 96 100 93 4713 1775 1.46 .685 .777 .626 .654 2.27 32 176 .658 .99 60 2020 40270 146 152 137 143 0 2169 253 1916 .685 1029 776 1.46 .777 -.546 -.364
19 6025 7546 311 248 5714 7298 5203 6641 404 352 4892 6393 0 0 2436 3497 314 332 100 100 100 100 13012 11285 .783 1.277 1.307 1.241 1.247 1.142 52 420 1.311 .99 90 2260 40230 140 149 159 168 0 7546 248 7298 1.277 6641 6393 .783 1.307 .353 .386
20 1213 1268 316 263 897 1005 545 585 332 273 229 322 0 0 1226 1338 131 103 58 57 48 55 1902 551 .893 1.12 1.406 1.09 1.071 1.886 80 560 1.106 .97 100 2500 40260 143 153 183 193 0 1268 263 1005 1.12 585 322 .893 1.406 .164 .492

Total number of rows: 4608

Table truncated, full table size 1104 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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