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Sample GSM78783 Query DataSets for GSM78783
Status Public on Oct 20, 2005
Title M1.16 genomic vs Tigr/Astra Ref 3
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 M1.16 genomic
Organism Helicobacter pylori
Characteristics 2 ug M1.16 genomic
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7911.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 6678 7118 277 482 6401 6636 null null 286 506 null null null null null null null null 100 100 null null null null .965 1.037 null null 1.056 null 52 420 .996 .97 null null null 69 78 88 97 0 7997 541 7456 1.165 null null .859 null .22 null .22
2 3785 1319 270 486 3515 833 null null 277 491 null null null null null null null null 98 90 null null null null 4.22 .237 null null .264 null 80 560 .213 .92 null null null 70 80 112 122 0 1482 546 936 .266 null null 3.755 null -1.909 null -1.909
3 2632 3246 298 549 2334 2697 null null 322 559 null null null null null null null null 100 100 null null null null .865 1.156 null null 1.096 null 32 236 1.047 .95 null null null 70 77 136 143 0 3647 616 3031 1.299 null null .77 null .377 null .377
4 370 726 297 585 73 141 null null 294 577 null null null null null null null null 57 66 null null null null .518 1.932 null null 4.268 null 12 68 .371 .27 null null null 72 76 163 167 0 815 657 158 2.164 null null .462 null 1.114 null 1.114
5 384 846 279 561 105 285 null null 282 566 null null null null null null null null 62 81 null null null null .368 2.714 null null 2.89 null 32 170 1.143 .62 null null null 71 77 186 192 0 950 630 320 3.048 null null .328 null 1.608 null 1.608
6 1096 895 287 590 809 305 null null 292 597 null null null null null null null null 82 86 null null null null 2.652 .377 null null .425 null 52 340 .232 .74 null null null 71 79 209 217 0 1005 662 343 .424 null null 2.359 null -1.238 null -1.238
7 1068 1190 321 663 747 527 null null 324 667 null null null null null null null null 100 83 null null null null 1.417 .705 null null .874 null 12 104 .653 .75 null null null 71 76 234 239 0 1337 744 593 .794 null null 1.26 null -.333 null -.333
8 760 1265 309 653 451 612 null null 312 659 null null null null null null null null 100 100 null null null null .737 1.357 null null 1.251 null 12 104 1.202 .83 null null null 72 77 257 262 0 1421 733 688 1.525 null null .656 null .609 null .609
9 2733 2666 336 741 2397 1925 null null 360 754 null null null null null null null null 96 94 null null null null 1.245 .803 null null .749 null 52 340 .735 .95 null null null 72 80 281 289 0 2995 832 2163 .902 null null 1.108 null -.148 null -.148
10 383 893 364 765 19 128 null null 375 785 null null null null null null null null 16 41 null null null null .148 6.737 null null 2.568 null 12 90 .867 .45 null null null 70 75 301 306 0 1003 859 144 7.579 null null .132 null 2.922 null 2.922
11 446 927 331 773 115 154 null null 338 781 null null null null null null null null 43 38 null null null null .747 1.339 null null 1.988 null 120 810 .921 .71 null null null 69 81 327 339 0 1041 868 173 1.504 null null .665 null .589 null .589
12 4675 7769 375 884 4300 6885 null null 387 906 null null null null null null null null 98 100 null null null null .625 1.601 null null 1.545 null 52 340 1.509 .96 null null null 73 81 354 362 0 8729 993 7736 1.799 null null .556 null .847 null .847
13 1449 1797 364 901 1085 896 null null 366 915 null null null null null null null null 95 95 null null null null 1.211 .826 null null .826 null 80 656 .746 .86 null null null 71 82 378 389 0 2019 1012 1007 .928 null null 1.077 null -.108 null -.108
14 3306 4121 376 958 2930 3163 null null 378 962 null null null null null null null null 100 100 null null null null .926 1.08 null null 1.001 null 32 236 .99 .91 null null null 73 80 401 408 0 4630 1076 3554 1.213 null null .824 null .279 null .279
15 1357 2714 364 942 993 1772 null null 374 965 null null null null null null null null 100 97 null null null null .56 1.784 null null 1.907 null 120 820 1.759 .9 null null null 71 83 424 436 0 3049 1058 1991 2.005 null null .499 null 1.004 null 1.004
16 778 1561 385 1000 393 561 null null 391 1005 null null null null null null null null 83 91 null null null null .701 1.427 null null 1.433 null 12 104 1.181 .95 null null null 75 80 452 457 0 1753 1123 630 1.603 null null .624 null .681 null .681
17 1382 2184 371 971 1011 1213 null null 402 1029 null null null null null null null null 100 87 null null null null .833 1.2 null null 1.189 null 32 236 1.112 .91 null null null 73 80 474 481 0 2453 1091 1362 1.347 null null .742 null .43 null .43
18 533 788 246 440 287 348 null null 262 452 null null null null null null null null 61 86 null null null null .825 1.213 null null 1.335 null 52 420 .805 .69 null null null 93 102 89 98 0 885 494 391 1.362 null null .734 null .446 null .446
19 1475 1244 257 460 1218 784 null null 262 467 null null null null null null null null 98 96 null null null null 1.554 .644 null null .627 null 52 340 .476 .8 null null null 93 101 113 121 0 1397 516 881 .723 null null 1.383 null -.467 null -.467
20 377 741 271 493 106 248 null null 279 504 null null null null null null null null 66 91 null null null null .427 2.34 null null 2.137 null 12 104 .667 .46 null null null 94 99 136 141 0 832 553 279 2.632 null null .38 null 1.396 null 1.396

Total number of rows: 4608

Table truncated, full table size 1156 Kbytes.




Supplementary data files not provided
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