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Sample GSM78741 Query DataSets for GSM78741
Status Public on Oct 20, 2005
Title 27616 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 27616 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug 27616 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-12/11922.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 11163 11237 1430 1022 9733 10215 null null 1451 1056 null null null null null null null null 95 96 null null null null .953 1.05 null null .989 null 80 552 .923 .95 null null null 85 95 63 73 0 11705 1064 10641 1.093 null null .915 null .129 null .129
2 6349 2245 1666 1178 4683 1067 null null 1708 1223 null null null null null null null null 95 72 null null null null 4.389 .228 null null .237 null 80 656 .261 .87 null null null 83 94 87 98 0 2338 1227 1111 .237 null null 4.215 null -2.076 null -2.076
3 10833 10201 1784 1335 9049 8866 null null 1839 1390 null null null null null null null null 93 95 null null null null 1.021 .98 null null .959 null 80 552 .94 .96 null null null 84 94 112 122 0 10626 1390 9236 1.021 null null .98 null .03 null .03
4 2572 2346 1698 1274 874 1072 null null 1733 1319 null null null null null null null null 43 50 null null null null .815 1.227 null null .884 null 32 236 .869 .9 null null null 85 92 140 147 0 2443 1327 1116 1.277 null null .783 null .353 null .353
5 2183 2193 1934 1417 249 776 null null 1976 1458 null null null null null null null null 28 31 null null null null .321 3.116 null null .866 null 32 236 .888 .89 null null null 85 92 164 171 0 2284 1476 808 3.245 null null .308 null 1.698 null 1.698
6 11587 6035 2016 1497 9571 4538 null null 2092 1561 null null null null null null null null 96 93 null null null null 2.109 .474 null null .443 null 80 648 .493 .93 null null null 82 93 184 195 0 6286 1559 4727 .494 null null 2.025 null -1.018 null -1.018
7 2082 1806 2070 1566 12 240 null null 2504 1884 null null null null null null null null 0 8 null null null null .05 20 null null 1.076 null 12 104 .762 .92 null null null 86 91 211 216 -100 1881 1631 250 20.833 null null .048 null null 4.381
8 1696 1195 1836 1551 -140 -356 null null 2365 2030 null null null null null null null null 0 0 null null null null null null null null .933 null 12 98 .865 .97 null null null 85 90 236 241 -100 1244 1615 -371 null null null null null null null
9 8119 7837 2100 1680 6019 6157 null null 2146 1720 null null null null null null null null 96 93 null null null null .978 1.023 null null 1.033 null 80 538 1.009 .97 null null null 83 93 257 267 0 8163 1750 6413 1.065 null null .939 null .091 null .091
10 4328 3979 2054 1683 2274 2296 null null 2114 1716 null null null null null null null null 40 43 null null null null .99 1.01 null null 1.028 null 32 160 .878 .89 null null null 84 90 284 290 0 4144 1753 2391 1.051 null null .951 null .072 null .072
11 4790 4750 2170 1612 2620 3138 null null 2177 1679 null null null null null null null null 53 78 null null null null .835 1.198 null null 1.083 null 32 230 .883 .92 null null null 83 90 306 313 0 4947 1679 3268 1.247 null null .802 null .319 null .319
12 8048 2007 2197 1688 5851 319 null null 2270 1762 null null null null null null null null 93 23 null null null null 18.342 .055 null null .108 null 80 552 .128 .54 null null null 83 93 328 338 0 2090 1758 332 .057 null null 17.623 null -4.139 null -4.139
13 4307 3661 2245 1843 2062 1818 null null 2262 1890 null null null null null null null null 80 78 null null null null 1.134 .882 null null .897 null 80 656 .842 .94 null null null 82 93 351 362 0 3813 1919 1894 .919 null null 1.089 null -.123 null -.123
14 9302 12236 2377 2005 6925 10231 null null 2879 2627 null null null null null null null null 56 67 null null null null .677 1.477 null null 1.429 null 80 538 1.437 .96 null null null 82 92 377 387 0 12745 2088 10657 1.539 null null .65 null .622 null .622
15 3306 2941 2013 1657 1293 1284 null null 2064 1712 null null null null null null null null 59 50 null null null null 1.007 .993 null null .965 null 32 220 .826 .88 null null null 82 89 403 410 0 3063 1726 1337 1.034 null null .967 null .048 null .048
16 5174 6324 1990 1652 3184 4672 null null 2042 1718 null null null null null null null null 90 96 null null null null .682 1.467 null null 1.453 null 32 220 .877 .81 null null null 82 89 426 433 0 6587 1720 4867 1.529 null null .654 null .612 null .612
17 4753 4251 1936 1531 2817 2720 null null 1972 1592 null null null null null null null null 76 71 null null null null 1.036 .966 null null .82 null 52 400 .92 .95 null null null 81 90 449 458 0 4428 1594 2834 1.006 null null .994 null .009 null .009
18 3571 3286 1440 1103 2131 2183 null null 1511 1161 null null null null null null null null 82 82 null null null null .976 1.024 null null .972 null 52 340 .923 .95 null null null 110 118 66 74 0 3422 1148 2274 1.067 null null .937 null .094 null .094
19 5378 4468 2064 1555 3314 2913 null null 2161 1619 null null null null null null null null 90 96 null null null null 1.138 .879 null null .825 null 32 176 .831 .95 null null null 110 116 90 96 0 4654 1619 3035 .916 null null 1.092 null -.127 null -.127
20 2623 2089 2001 1560 622 529 null null 2017 1563 null null null null null null null null 46 31 null null null null 1.176 .85 null null .649 null 32 236 .671 .83 null null null 109 116 114 121 0 2176 1625 551 .886 null null 1.129 null -.175 null -.175

Total number of rows: 4608

Table truncated, full table size 1173 Kbytes.




Supplementary data files not provided
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