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Sample GSM78728 Query DataSets for GSM78728
Status Public on Oct 20, 2005
Title 314a vs Tigr/Astra Reference
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 314a genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug 314a genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11916.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 8411 8237 1482 1157 6929 7080 null null 1509 1195 null null null null null null null null 100 100 null null null null .979 1.022 null null .973 null 32 236 .961 .98 null null null 33 40 37 44 0 8075 1134 6941 1.002 null null .998 null .002 null .002
2 5550 1891 1483 1188 4067 703 null null 1522 1217 null null null null null null null null 100 78 null null null null 5.785 .173 null null .269 null 32 236 .109 .64 null null null 32 39 60 67 0 1853 1164 689 .169 null null 5.903 null -2.561 null -2.561
3 11007 9679 1540 1263 9467 8416 null null 1553 1326 null null null null null null null null 100 100 null null null null 1.125 .889 null null .939 null 52 340 .832 .91 null null null 32 40 86 94 0 9489 1238 8251 .872 null null 1.147 null -.198 null -.198
4 2672 2130 1451 1292 1221 838 null null 1459 1321 null null null null null null null null 87 75 null null null null 1.457 .686 null null .696 null 32 236 .504 .64 null null null 31 38 110 117 0 2088 1266 822 .673 null null 1.485 null -.571 null -.571
5 2876 1767 1582 1210 1294 557 null null 1587 1285 null null null null null null null null 100 66 null null null null 2.323 .43 null null .525 null 12 68 .272 .54 null null null 34 38 136 140 0 1732 1186 546 .422 null null 2.37 null -1.245 null -1.245
6 7129 4062 1540 1260 5589 2802 null null 1555 1271 null null null null null null null null 100 98 null null null null 1.995 .501 null null .46 null 52 332 .473 .9 null null null 31 39 158 166 0 3982 1235 2747 .492 null null 2.035 null -1.025 null -1.025
7 2111 1651 1553 1258 558 393 null null 1556 1283 null null null null null null null null 65 53 null null null null 1.42 .704 null null .976 null 32 236 .413 .47 null null null 31 38 182 189 0 1618 1233 385 .69 null null 1.449 null -.535 null -.535
8 2696 1814 1592 1243 1104 571 null null 1612 1349 null null null null null null null null 91 41 null null null null 1.933 .517 null null .517 null 12 98 .458 .48 null null null 31 36 206 211 0 1778 1218 560 .507 null null 1.971 null -.979 null -.979
9 5572 4984 1578 1350 3994 3634 null null 1662 1405 null null null null null null null null 82 90 null null null null 1.099 .91 null null .937 null 52 420 .911 .96 null null null 30 39 228 237 0 4886 1323 3563 .892 null null 1.121 null -.165 null -.165
10 2478 2274 1581 1335 897 939 null null 1587 1389 null null null null null null null null 90 80 null null null null .955 1.047 null null 1.071 null 52 340 .683 .63 null null null 31 39 254 262 0 2229 1308 921 1.027 null null .974 null .038 null .038
11 2422 2128 1593 1317 829 811 null null 1618 1340 null null null null null null null null 81 67 null null null null 1.022 .978 null null 1.13 null 80 560 .644 .66 null null null 31 41 276 286 0 2086 1291 795 .959 null null 1.043 null -.06 null -.06
12 7206 1526 1654 1352 5552 174 null null 1675 1364 null null null null null null null null 98 26 null null null null 31.908 .031 null null .062 null 52 420 .039 .35 null null null 29 38 300 309 0 1496 1325 171 .031 null null 32.468 null -5.021 null -5.021
13 3715 3174 1634 1446 2081 1728 null null 1631 1459 null null null null null null null null 98 82 null null null null 1.204 .83 null null .879 null 52 340 .683 .81 null null null 31 39 324 332 0 3111 1417 1694 .814 null null 1.228 null -.297 null -.297
14 7721 9655 1563 1370 6158 8285 null null 1571 1403 null null null null null null null null 100 100 null null null null .743 1.345 null null 1.332 null 52 420 1.194 .92 null null null 29 38 347 356 0 9465 1343 8122 1.319 null null .758 null .399 null .399
15 3568 2588 1497 1375 2071 1213 null null 1520 1408 null null null null null null null null 86 80 null null null null 1.707 .586 null null .708 null 52 332 .481 .89 null null null 30 38 374 382 0 2537 1348 1189 .574 null null 1.742 null -.801 null -.801
16 3394 3280 1555 1397 1839 1883 null null 1553 1427 null null null null null null null null 100 88 null null null null .977 1.024 null null 1.182 null 52 412 .822 .83 null null null 28 37 396 405 0 3215 1369 1846 1.004 null null .996 null .005 null .005
17 6115 6506 1641 1511 4474 4995 null null 1666 1557 null null null null null null null null 98 100 null null null null .896 1.116 null null 1.02 null 52 420 .988 .92 null null null 29 38 421 430 0 6378 1481 4897 1.095 null null .914 null .13 null .13
18 3905 3840 1510 1238 2395 2602 null null 1508 1270 null null null null null null null null 86 84 null null null null .92 1.086 null null .983 null 52 420 .971 .94 null null null 55 64 37 46 0 3764 1213 2551 1.065 null null .939 null .091 null .091
19 4274 3352 1501 1239 2773 2113 null null 1497 1253 null null null null null null null null 98 98 null null null null 1.312 .762 null null .763 null 52 340 .683 .92 null null null 56 64 61 69 0 3286 1214 2072 .747 null null 1.338 null -.42 null -.42
20 2878 1782 1619 1320 1259 462 null null 1620 1356 null null null null null null null null 91 50 null null null null 2.725 .367 null null .934 null 12 68 .267 .43 null null null 57 61 89 93 0 1747 1294 453 .36 null null 2.779 null -1.475 null -1.475

Total number of rows: 4608

Table truncated, full table size 1169 Kbytes.




Supplementary data files not provided
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