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Sample GSM78726 Query DataSets for GSM78726
Status Public on Oct 20, 2005
Title 29061 vs Tigr/Astra Reference 2
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA + 1ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 1ug Tigr genomic DNA + 1ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug 29061 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug 29061 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11914.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 19, 2005
Last update date Feb 20, 2008
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)
GSE3479 Helicobacter pylori bacterial populations

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 3131 3994 1111 1083 2020 2911 null null 1117 1118 null null null null null null null null 94 96 null null null null .694 1.441 null null 1.538 null 52 420 1.243 .94 null null null 38 47 40 49 0 3384 917 2467 1.221 null null .819 null .288 null .288
2 3398 1331 1183 1139 2215 192 null null 1198 1150 null null null null null null null null 98 44 null null null null 11.536 .087 null null .173 null 52 412 .061 .28 null null null 36 45 65 74 0 1127 965 162 .073 null null 13.673 null -3.773 null -3.773
3 3199 3591 1202 1212 1997 2379 null null 1210 1219 null null null null null null null null 95 95 null null null null .839 1.191 null null 1.172 null 80 560 1.148 .96 null null null 37 47 88 98 0 3043 1027 2016 1.01 null null .991 null .014 null .014
4 5020 7543 1225 1264 3795 6279 null null 1279 1364 null null null null null null null null 96 95 null null null null .604 1.655 null null 1.61 null 80 543 1.574 .97 null null null 30 41 111 122 -100 6392 1071 5321 1.402 null null .713 null null .488
5 1303 1313 1136 1079 167 234 null null 1159 1110 null null null null null null null null 31 37 null null null null .714 1.401 null null 1.245 null 120 779 .414 .41 null null null 36 48 133 145 0 1112 914 198 1.186 null null .843 null .246 null .246
6 3706 1961 1073 915 2633 1046 null null 1087 928 null null null null null null null null 92 88 null null null null 2.517 .397 null null .375 null 52 340 .375 .89 null null null 38 46 161 169 0 1661 775 886 .336 null null 2.972 null -1.571 null -1.571
7 1714 1338 1153 984 561 354 null null 1153 979 null null null null null null null null 75 57 null null null null 1.585 .631 null null .698 null 12 104 .435 .52 null null null 39 44 188 193 0 1133 833 300 .535 null null 1.87 null -.903 null -.903
8 1564 1614 1288 1148 276 466 null null 1391 1229 null null null null null null null null 25 75 null null null null .592 1.688 null null 1.505 null 12 68 .232 .25 null null null 40 44 215 219 0 1367 972 395 1.431 null null .699 null .517 null .517
9 3435 3866 1288 1291 2147 2575 null null 1295 1308 null null null null null null null null 90 92 null null null null .834 1.199 null null 1.173 null 52 340 1.013 .91 null null null 38 46 233 241 0 3276 1094 2182 1.016 null null .984 null .023 null .023
10 1789 1955 1260 1266 529 689 null null 1272 1275 null null null null null null null null 76 78 null null null null .768 1.302 null null 1.427 null 52 412 .776 .59 null null null 36 45 255 264 0 1656 1072 584 1.104 null null .906 null .143 null .143
11 2790 2451 1477 1538 1313 913 null null 1464 1534 null null null null null null null null 83 66 null null null null 1.438 .695 null null .932 null 12 68 .807 .84 null null null 40 44 283 287 0 2077 1303 774 .589 null null 1.696 null -.762 null -.762
12 4551 1487 1287 1294 3264 193 null null 1315 1304 null null null null null null null null 100 40 null null null null 16.912 .059 null null .121 null 52 412 .015 .09 null null null 36 45 304 313 0 1260 1096 164 .05 null null 19.902 null -4.315 null -4.315
13 2624 3006 1359 1311 1265 1695 null null 1377 1318 null null null null null null null null 94 92 null null null null .746 1.34 null null 1.245 null 52 340 1.184 .86 null null null 39 47 327 335 0 2547 1111 1436 1.135 null null .881 null .183 null .183
14 4804 7827 1352 1332 3452 6495 null null 1369 1345 null null null null null null null null 94 100 null null null null .531 1.882 null null 1.931 null 52 420 1.714 .95 null null null 37 46 351 360 0 6633 1128 5505 1.595 null null .627 null .673 null .673
15 4414 3619 1473 1552 2941 2067 null null 1493 1573 null null null null null null null null 100 91 null null null null 1.423 .703 null null .743 null 12 104 .58 .84 null null null 39 44 377 382 -100 3066 1315 1751 .595 null null 1.68 null null -.748
16 2485 2918 1318 1347 1167 1571 null null 1331 1386 null null null null null null null null 90 86 null null null null .743 1.346 null null 1.346 null 52 400 1.262 .93 null null null 35 44 399 408 -100 2472 1141 1331 1.141 null null .877 null null .19
17 4935 5139 1345 1326 3590 3813 null null 1346 1350 null null null null null null null null 100 98 null null null null .942 1.062 null null 1.441 null 52 324 .367 .63 null null null 37 45 425 433 0 4355 1123 3232 .9 null null 1.111 null -.152 null -.152
18 2500 2393 1184 1229 1316 1164 null null 1188 1263 null null null null null null null null 65 56 null null null null 1.131 .884 null null .843 null 32 176 .804 .92 null null null 64 70 43 49 0 2027 1041 986 .749 null null 1.335 null -.417 null -.417
19 2997 2724 1198 1167 1799 1557 null null 1194 1182 null null null null null null null null 98 96 null null null null 1.155 .865 null null .843 null 52 420 .843 .93 null null null 61 70 64 73 0 2308 988 1320 .734 null null 1.363 null -.447 null -.447
20 1477 1459 1216 1202 261 257 null null 1234 1239 null null null null null null null null 45 33 null null null null 1.016 .985 null null .981 null 120 767 .738 .58 null null null 60 72 86 98 0 1236 1018 218 .835 null null 1.197 null -.26 null -.26

Total number of rows: 4608

Table truncated, full table size 1164 Kbytes.




Supplementary data files not provided
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