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Sample GSM78674 Query DataSets for GSM78674
Status Public on Oct 20, 2005
Title J99-C10 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 J99-C10 genomic
Organism Helicobacter pylori
Characteristics 2 ug J99-C10 genomic
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10861.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 6554 4745 1230 1512 5324 3233 null null 1246 1567 null null null null null null null null 98 90 null null null null 1.647 .607 null null .629 null 52 332 .564 .92 null null null 42 50 59 67 0 6412 2043 4369 .821 null null 1.219 null -.285 null -.285
2 4371 2521 1265 1527 3106 994 null null 1290 1569 null null null null null null null null 93 65 null null null null 3.125 .32 null null .437 null 32 176 .234 .77 null null null 42 48 85 91 0 3406 2063 1343 .432 null null 2.313 null -1.21 null -1.21
3 8360 5757 1267 1535 7093 4222 null null 1288 1572 null null null null null null null null 100 100 null null null null 1.68 .595 null null .526 null 32 236 .6 .92 null null null 41 48 108 115 0 7779 2074 5705 .804 null null 1.243 null -.314 null -.314
4 1637 1696 1252 1542 385 154 null null 1273 1567 null null null null null null null null 25 30 null null null null 2.5 .4 null null 1.347 null 120 794 .262 .36 null null null 37 49 129 141 0 2291 2083 208 .54 null null 1.851 null -.888 null -.888
5 2552 2078 1232 1693 1320 385 null null 1454 1764 null null null null null null null null 31 34 null null null null 3.429 .292 null null .746 null 32 170 .246 .56 null null null 40 46 158 164 0 2808 2287 521 .395 null null 2.534 null -1.341 null -1.341
6 10449 3451 1251 1608 9198 1843 null null 1287 1576 null null null null null null null null 100 78 null null null null 4.991 .2 null null .208 null 32 176 .185 .86 null null null 41 47 182 188 0 4663 2172 2491 .271 null null 3.692 null -1.885 null -1.885
7 3614 2998 1230 1643 2384 1355 null null 1297 1676 null null null null null null null null 100 91 null null null null 1.759 .568 null null .808 null 12 104 .392 .63 null null null 40 45 205 210 0 4051 2220 1831 .768 null null 1.302 null -.381 null -.381
8 3300 2548 1191 1625 2109 923 null null 1178 1654 null null null null null null null null 91 66 null null null null 2.285 .438 null null .539 null 12 68 .278 .61 null null null 42 46 231 235 0 3443 2195 1248 .592 null null 1.69 null -.757 null -.757
9 9370 5538 1358 1773 8012 3765 null null 1401 1784 null null null null null null null null 100 83 null null null null 2.128 .47 null null .44 null 12 104 .519 .91 null null null 40 45 253 258 0 7483 2395 5088 .635 null null 1.575 null -.655 null -.655
10 2734 2978 1311 1750 1423 1228 null null 1348 1733 null null null null null null null null 100 100 null null null null 1.159 .863 null null .749 null 12 68 .594 .57 null null null 42 46 278 282 0 4024 2364 1660 1.167 null null .857 null .222 null .222
11 3380 3046 1254 1691 2126 1355 null null 1266 1711 null null null null null null null null 93 78 null null null null 1.569 .637 null null .706 null 32 176 .487 .74 null null null 41 47 301 307 0 4116 2285 1831 .861 null null 1.161 null -.216 null -.216
12 5774 2882 1372 1703 4402 1179 null null 1378 1760 null null null null null null null null 96 87 null null null null 3.734 .268 null null .266 null 32 170 .219 .7 null null null 40 46 325 331 0 3894 2301 1593 .362 null null 2.763 null -1.466 null -1.466
13 4799 5357 1310 1750 3489 3607 null null 1321 1788 null null null null null null null null 100 96 null null null null .967 1.034 null null 1.012 null 32 236 .896 .85 null null null 40 47 347 354 0 7239 2364 4875 1.397 null null .716 null .483 null .483
14 10912 5973 1339 1772 9573 4201 null null 1340 1786 null null null null null null null null 100 98 null null null null 2.279 .439 null null .407 null 52 340 .44 .93 null null null 40 48 371 379 0 8071 2394 5677 .593 null null 1.686 null -.754 null -.754
15 4573 3422 1280 1865 3293 1557 null null 1339 1909 null null null null null null null null 100 75 null null null null 2.115 .473 null null .499 null 12 104 .478 .82 null null null 40 45 396 401 0 4624 2520 2104 .639 null null 1.565 null -.646 null -.646
16 3973 3402 1303 1753 2670 1649 null null 1298 1795 null null null null null null null null 96 93 null null null null 1.619 .618 null null .776 null 32 236 .464 .78 null null null 40 47 420 427 0 4597 2368 2229 .835 null null 1.198 null -.26 null -.26
17 8504 10314 1282 1823 7222 8491 null null 1336 1855 null null null null null null null null 100 100 null null null null .851 1.176 null null 1.06 null 32 236 1.167 .96 null null null 40 47 443 450 0 13937 2463 11474 1.589 null null .629 null .668 null .668
18 5703 3886 1331 1588 4372 2298 null null 1386 1608 null null null null null null null null 100 91 null null null null 1.903 .526 null null .506 null 12 104 .429 .75 null null null 64 69 61 66 0 5251 2145 3106 .71 null null 1.408 null -.493 null -.493
19 5140 3842 1318 1552 3822 2290 null null 1333 1588 null null null null null null null null 96 90 null null null null 1.669 .599 null null .561 null 32 176 .51 .84 null null null 64 70 86 92 0 5191 2097 3094 .81 null null 1.235 null -.305 null -.305
20 4138 3044 1311 1536 2827 1508 null null 1302 1599 null null null null null null null null 91 91 null null null null 1.875 .533 null null .596 null 12 68 .332 .72 null null null 66 70 111 115 0 4113 2075 2038 .721 null null 1.387 null -.472 null -.472

Total number of rows: 4608

Table truncated, full table size 1170 Kbytes.




Supplementary data files not provided
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