NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM184252 Query DataSets for GSM184252
Status Public on Aug 09, 2007
Title 249c6
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 249c6
Organism Helicobacter pylori
Characteristics 0.25 ug 249c6
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/2002-08/32369.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 2535 4518 148 164 2387 4354 2215 4407 183 224 2067 4243 0 0 1220 2188 120 228 100 100 100 100 6741 6310 .548 1.824 2.053 1.822 1.715 1.338 32 206 1.882 .95 70 1840 42550 143 150 92 99 0 3734 136 3598 1.507 3642 3507 .663 1.696 .592 .763
2 2229 445 293 186 1936 259 2140 454 469 203 1847 268 0 0 981 163 343 77 100 75 100 75 2195 2115 7.475 .134 .145 .119 .142 1.685 4 20 .13 .86 30 2120 42550 145 148 122 125 0 368 154 214 .111 375 221 9.045 .12 -3.177 -3.06
3 3737 4379 175 165 3562 4214 4131 5272 208 205 3956 5107 0 0 1522 1954 120 120 100 100 100 100 7776 9063 .845 1.183 1.291 1.127 1.182 1.393 12 98 1.18 .94 50 2330 42540 143 148 142 147 0 3619 136 3483 .978 4357 4221 1.023 1.067 -.033 .093
4 164 166 132 124 32 42 151 151 133 127 19 27 0 0 57 66 30 29 38 46 20 32 74 46 .762 1.313 1.421 1.336 1.152 3.185 80 552 1.274 .34 100 2580 42540 141 151 165 175 0 137 102 35 1.085 125 22 .922 1.174 .117 .232
5 147 140 130 121 17 19 137 136 132 124 7 15 0 0 46 46 28 29 30 33 15 15 36 22 .895 1.118 2.143 .92 .9 2.994 80 552 1.133 .28 100 2820 42540 141 151 189 199 0 116 100 16 .924 112 12 1.083 1.771 -.115 .825
6 3094 2380 140 132 2954 2248 2754 2252 150 135 2614 2120 0 0 1998 1570 61 35 100 100 100 100 5202 4734 1.314 .761 .811 .739 .772 1.461 32 170 .748 .94 60 3070 42540 143 149 216 222 0 1967 109 1858 .629 1861 1752 1.59 .67 -.669 -.577
7 364 400 135 125 229 275 226 237 139 130 91 112 0 0 285 328 35 37 76 72 58 58 504 203 .833 1.201 1.231 1.003 1.079 2.853 80 552 1.173 .93 100 3310 42540 141 151 238 248 0 331 103 227 .992 196 93 1.008 1.017 -.011 .025
8 164 168 127 119 37 49 149 141 130 120 22 22 0 0 76 109 29 29 40 45 25 26 86 44 .755 1.324 1 1.211 1.258 3.005 80 552 1.538 .65 100 3550 42540 141 151 262 272 0 139 98 40 1.094 117 18 .914 .826 .13 -.275
9 1427 2149 133 131 1294 2018 1246 1870 149 167 1113 1739 0 0 970 1441 73 124 100 100 100 100 3312 2852 .641 1.56 1.562 1.586 1.604 1.446 32 148 1.581 .93 60 3800 42520 141 147 289 295 0 1776 108 1668 1.289 1545 1437 .776 1.291 .366 .369
10 219 278 131 114 88 164 171 204 132 115 40 90 0 0 123 177 29 29 57 75 43 60 252 130 .537 1.864 2.25 1.699 1.759 2.703 80 538 1.646 .82 100 4030 42530 140 150 310 320 0 230 94 136 1.54 169 74 .649 1.86 .623 .895
11 207 244 135 113 72 131 156 178 135 114 21 65 0 0 121 187 30 28 46 65 32 53 203 86 .55 1.819 3.095 1.732 1.543 3.241 80 522 1.703 .75 100 4270 42520 139 149 334 344 0 202 93 108 1.504 147 54 .665 2.558 .588 1.355
12 1296 264 157 119 1139 145 1328 265 206 127 1171 146 0 0 788 94 151 41 84 78 84 65 1284 1317 7.855 .127 .125 .149 .134 2.033 32 134 .113 .76 60 4480 42510 140 146 357 363 0 218 98 120 .105 219 121 9.505 .103 -3.249 -3.279
13 1753 2345 164 162 1589 2183 1727 2210 215 242 1563 2048 0 0 483 631 141 197 100 100 100 100 3772 3611 .728 1.374 1.31 1.397 1.343 1.281 52 288 1.372 .94 80 4750 42510 139 147 383 391 0 1938 134 1804 1.135 1826 1693 .881 1.083 .183 .115
14 3385 6440 172 169 3213 6271 3607 6558 179 200 3435 6389 0 0 1548 3014 55 95 100 100 100 100 9484 9824 .512 1.952 1.86 1.971 1.899 1.637 32 148 1.996 .95 60 4970 42520 141 147 406 412 0 5322 140 5183 1.613 5420 5280 .62 1.537 .69 .62
15 614 792 142 127 472 665 378 396 145 134 236 269 0 0 634 836 34 42 78 87 70 80 1137 505 .71 1.409 1.14 1.364 1.322 2.568 80 522 1.373 .93 100 5230 42520 139 149 430 440 0 655 105 550 1.164 327 222 .859 .942 .22 -.086
16 1446 1440 174 147 1272 1293 1424 1237 191 153 1250 1090 0 0 429 614 60 65 100 100 100 100 2565 2340 .984 1.017 .872 .985 1.135 1.59 4 14 1.073 .9 30 5460 42530 143 146 456 459 0 1190 121 1069 .84 1022 901 1.19 .721 -.251 -.473
17 969 879 138 123 831 756 809 810 148 132 671 687 0 0 638 639 47 54 100 96 96 87 1587 1358 1.099 .91 1.024 .824 .852 1.701 32 148 .952 .88 60 5700 42520 141 147 479 485 0 726 102 625 .752 669 568 1.33 .846 -.411 -.241
18 3113 2064 196 172 2917 1892 3187 1945 213 184 2991 1773 0 0 1403 682 65 53 100 100 100 100 4809 4764 1.542 .649 .593 .682 .737 1.282 4 20 .639 .92 30 1870 42770 167 170 97 100 0 1706 142 1564 .536 1607 1465 1.866 .49 -.9 -1.029
19 1580 1691 145 145 1435 1546 1567 1582 155 155 1422 1437 0 0 724 873 51 51 100 100 100 100 2981 2859 .928 1.077 1.011 1.047 1.067 1.345 80 560 1.119 .96 100 2110 42760 163 173 118 128 0 1398 120 1278 .89 1307 1188 1.123 .835 -.168 -.26
20 264 265 138 137 126 128 213 214 139 139 75 77 0 0 138 144 30 32 73 66 58 53 254 152 .984 1.016 1.027 .987 1.018 2.531 80 560 1.02 .81 100 2350 42760 163 173 142 152 0 219 113 106 .84 177 64 1.191 .848 -.252 -.237

Total number of rows: 4608

Table truncated, full table size 1067 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap