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Sample GSM78780 Query DataSets for GSM78780
Status Public on Oct 20, 2005
Title H15 vs. Tigr/Astra reference 2
Sample type genomic
 
Channel 1
Source name 1ug genomic DNATigr + 1 ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 1ug genomic DNATigr + 1 ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug H15 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug H15 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-08/8427.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 9107 6056 244 502 8863 5554 null null 249 531 null null null null null null null null 98 77 null null null null 1.596 .627 null null .622 null 120 756 .615 .94 null null null 59 71 45 57 0 9038 749 8289 .935 null null 1.069 null -.097 null -.097
2 3362 1050 232 491 3130 559 null null 237 524 null null null null null null null null 98 57 null null null null 5.599 .179 null null .202 null 120 892 .163 .77 null null null 58 71 67 80 0 1567 732 835 .267 null null 3.749 null -1.906 null -1.906
3 4102 2964 227 482 3875 2482 null null 240 513 null null null null null null null null 100 92 null null null null 1.561 .641 null null .66 null 52 420 .562 .92 null null null 60 69 93 102 0 4423 719 3704 .956 null null 1.046 null -.065 null -.065
4 246 480 220 478 26 2 null null 224 506 null null null null null null null null 27 14 null null null null 13 .077 null null 4.901 null 120 778 .322 .08 null null null 57 69 116 128 0 716 713 3 .115 null null 8.667 null -3.115 null -3.115
5 223 491 222 476 1 15 null null 230 518 null null null null null null null null 5 15 null null null null .067 15 null null 4.298 null 120 778 .251 .05 null null null 57 69 140 152 0 732 710 22 22 null null .045 null 4.459 null 4.459
6 2792 1360 218 459 2574 901 null null 220 493 null null null null null null null null 100 87 null null null null 2.857 .35 null null .324 null 32 176 .348 .88 null null null 62 68 168 174 0 2029 685 1344 .522 null null 1.915 null -.937 null -.937
7 340 564 228 476 112 88 null null 244 517 null null null null null null null null 25 21 null null null null 1.273 .786 null null 2.217 null 120 778 .441 .31 null null null 57 69 188 200 0 841 710 131 1.17 null null .855 null .226 null .226
8 306 557 236 507 70 50 null null 251 533 null null null null null null null null 20 15 null null null null 1.4 .714 null null 1.769 null 120 764 .939 .43 null null null 57 69 212 224 0 831 756 75 1.071 null null .933 null .1 null .1
9 2905 2064 248 525 2657 1539 null null 258 550 null null null null null null null null 93 73 null null null null 1.726 .579 null null .661 null 120 754 .509 .9 null null null 59 71 236 248 0 3080 783 2297 .865 null null 1.157 null -.21 null -.21
10 340 622 254 499 86 123 null null 277 550 null null null null null null null null 16 20 null null null null .699 1.43 null null 2.333 null 120 790 .873 .58 null null null 57 69 260 272 0 928 744 184 2.14 null null .467 null 1.097 null 1.097
11 842 1035 261 555 581 480 null null 264 574 null null null null null null null null 90 71 null null null null 1.21 .826 null null .836 null 32 176 .686 .67 null null null 63 69 288 294 0 1544 828 716 1.232 null null .811 null .301 null .301
12 8468 936 293 533 8175 403 null null 494 577 null null null null null null null null 100 63 null null null null 20.285 .049 null null .051 null 52 340 .044 .57 null null null 60 68 311 319 0 1397 795 602 .074 null null 13.58 null -3.763 null -3.763
13 3147 2290 271 510 2876 1780 null null 303 551 null null null null null null null null 93 87 null null null null 1.616 .619 null null .598 null 80 560 .56 .9 null null null 59 69 335 345 0 3417 761 2656 .924 null null 1.083 null -.115 null -.115
14 6158 4101 281 524 5877 3577 null null 295 556 null null null null null null null null 94 90 null null null null 1.643 .609 null null .599 null 52 340 .578 .92 null null null 61 69 359 367 0 6120 782 5338 .908 null null 1.101 null -.139 null -.139
15 876 836 246 521 630 315 null null 289 639 null null null null null null null null 59 15 null null null null 2 .5 null null .748 null 32 160 .38 .5 null null null 59 65 383 389 0 1247 777 470 .746 null null 1.34 null -.423 null -.423
16 415 639 288 577 127 62 null null 308 607 null null null null null null null null 28 22 null null null null 2.048 .488 null null 2.286 null 120 810 .526 .38 null null null 57 69 404 416 0 953 861 92 .724 null null 1.38 null -.465 null -.465
17 1388 1329 267 581 1121 748 null null 316 610 null null null null null null null null 91 91 null null null null 1.499 .667 null null .716 null 12 104 .577 .74 null null null 60 65 431 436 0 1983 867 1116 .996 null null 1.004 null -.006 null -.006
18 296 569 245 498 51 71 null null 250 521 null null null null null null null null 25 24 null null null null .718 1.392 null null 4.12 null 120 766 .291 .12 null null null 81 93 44 56 0 849 743 106 2.078 null null .481 null 1.055 null 1.055
19 4067 2052 244 511 3823 1541 null null 258 548 null null null null null null null null 100 90 null null null null 2.481 .403 null null .499 null 32 236 .324 .78 null null null 84 91 71 78 0 3062 762 2300 .602 null null 1.662 null -.733 null -.733
20 346 589 248 499 98 90 null null 266 538 null null null null null null null null 46 26 null null null null 1.089 .918 null null 1.341 null 120 774 .608 .39 null null null 81 93 92 104 0 879 744 135 1.378 null null .726 null .462 null .462

Total number of rows: 4608

Table truncated, full table size 1144 Kbytes.




Supplementary data files not provided

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