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Sample GSM78784 Query DataSets for GSM78784
Status Public on Oct 20, 2005
Title B128A genomic vs Tigr/Astra Ref 4
Sample type genomic
 
Channel 1
Source name 1ug Tigr genomic DNA + 1 ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 1ug Tigr genomic DNA + 1 ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug B128A genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug B128A genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7913.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 5556 3380 275 661 5281 2719 null null 280 663 null null null null null null null null 100 100 null null null null 1.942 .515 null null .484 null 52 288 .466 .91 null null null 71 79 98 106 0 4898 957 3941 .746 null null 1.34 null -.422 null -.422
2 3907 1170 274 617 3633 553 null null 283 615 null null null null null null null null 100 90 null null null null 6.57 .152 null null .165 null 52 420 .13 .86 null null null 71 80 123 132 0 1695 894 801 .22 null null 4.536 null -2.181 null -2.181
3 2531 2099 285 656 2246 1443 null null 306 658 null null null null null null null null 93 100 null null null null 1.556 .642 null null .724 null 32 236 .54 .93 null null null 71 78 146 153 0 3042 950 2092 .931 null null 1.074 null -.102 null -.102
4 306 703 268 652 38 51 null null 271 654 null null null null null null null null 30 26 null null null null .745 1.342 null null 1.847 null 120 779 .551 .37 null null null 68 80 171 183 0 1018 944 74 1.947 null null .514 null .962 null .962
5 288 731 277 730 11 1 null null 283 734 null null null null null null null null 15 16 null null null null 11 .091 null null 2.105 null 120 779 .508 .27 null null null 68 80 195 207 0 1059 1057 2 .182 null null 5.5 null -2.459 null -2.459
6 2095 1401 307 814 1788 587 null null 304 821 null null null null null null null null 100 100 null null null null 3.046 .328 null null .332 null 12 54 .263 .87 null null null 71 75 221 225 0 2030 1179 851 .476 null null 2.101 null -1.071 null -1.071
7 801 1187 304 856 497 331 null null 319 858 null null null null null null null null 100 83 null null null null 1.502 .666 null null .67 null 12 90 .504 .82 null null null 69 74 244 249 0 1720 1240 480 .966 null null 1.035 null -.05 null -.05
8 654 1130 311 791 343 339 null null 314 792 null null null null null null null null 84 87 null null null null 1.012 .988 null null 1.009 null 32 176 .584 .66 null null null 72 78 269 275 0 1637 1146 491 1.431 null null .699 null .518 null .518
9 3665 2848 338 839 3327 2009 null null 391 855 null null null null null null null null 96 96 null null null null 1.656 .604 null null .584 null 32 236 .5 .89 null null null 71 78 291 298 0 4127 1215 2912 .875 null null 1.143 null -.192 null -.192
10 390 919 324 862 66 57 null null 328 865 null null null null null null null null 35 27 null null null null 1.158 .864 null null 1.523 null 120 794 .704 .58 null null null 68 80 316 328 0 1331 1249 82 1.242 null null .805 null .313 null .313
11 404 956 342 932 62 24 null null 350 941 null null null null null null null null 24 15 null null null null 2.583 .387 null null 1.529 null 120 794 .555 .52 null null null 68 80 340 352 0 1385 1350 35 .565 null null 1.771 null -.825 null -.825
12 4516 4487 386 1063 4130 3424 null null 398 1070 null null null null null null null null 100 100 null null null null 1.206 .829 null null .861 null 52 340 .784 .96 null null null 71 79 366 374 0 6502 1540 4962 1.201 null null .832 null .265 null .265
13 1275 1778 369 1060 906 718 null null 376 1064 null null null null null null null null 96 90 null null null null 1.262 .792 null null .747 null 52 340 .647 .84 null null null 72 80 390 398 0 2576 1536 1040 1.148 null null .871 null .199 null .199
14 2654 2843 392 1137 2262 1706 null null 1181 1766 null null null null null null null null 0 0 null null null null 1.326 .754 null null .766 null 32 160 .789 .93 null null null 70 76 414 420 0 4120 1647 2473 1.093 null null .915 null .129 null .129
15 905 1723 377 1126 528 597 null null 390 1139 null null null null null null null null 100 94 null null null null .884 1.131 null null 1.424 null 52 340 .749 .68 null null null 72 80 440 448 0 2497 1631 866 1.64 null null .61 null .714 null .714
16 521 1332 393 1180 128 152 null null 392 1156 null null null null null null null null 25 17 null null null null .842 1.188 null null 1.176 null 120 784 .709 .56 null null null 68 80 461 473 0 1930 1710 220 1.719 null null .582 null .781 null .781
17 575 1306 407 1198 168 108 null null 420 1186 null null null null null null null null 24 20 null null null null 1.556 .643 null null 1.174 null 120 794 .671 .62 null null null 68 80 485 497 0 1892 1736 156 .929 null null 1.077 null -.107 null -.107
18 580 1005 266 603 314 402 null null 267 602 null null null null null null null null 88 98 null null null null .781 1.28 null null 1.367 null 52 332 .879 .85 null null null 92 100 101 109 0 1456 873 583 1.857 null null .539 null .893 null .893
19 1889 1140 266 586 1623 554 null null 268 591 null null null null null null null null 100 96 null null null null 2.93 .341 null null .315 null 32 176 .288 .86 null null null 94 100 127 133 0 1652 849 803 .495 null null 2.021 null -1.015 null -1.015
20 283 649 270 611 13 38 null null 275 613 null null null null null null null null 24 23 null null null null .342 2.923 null null 1.834 null 120 804 .324 .18 null null null 92 104 148 160 0 940 885 55 4.231 null null .236 null 2.081 null 2.081

Total number of rows: 4608

Table truncated, full table size 1158 Kbytes.




Supplementary data files not provided

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