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Sample GSM73602 Query DataSets for GSM73602
Status Public on Sep 09, 2005
Title CA23 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 CA23genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug CA23genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10865.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 Sep 08, 2005
Last update date Sep 22, 2006
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 (2)
GSE3272 Mouse response to H. pylory
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 values 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 value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value 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 value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value 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 5933 6054 783 539 5150 5515 null null 811 572 null null null null null null null null 98 100 null null null null .934 1.071 null null 1.049 null 80 648 1.144 .98 null null null 115 126 99 110 0 7761 691 7070 1.373 null null .728 null .457 null .457
2 3781 1016 777 505 3004 511 null null 786 537 null null null null null null null null 100 80 null null null null 5.879 .17 null null .174 null 52 340 .144 .84 null null null 116 124 125 133 0 1302 647 655 .218 null null 4.586 null -2.197 null -2.197
3 8570 9217 748 495 7822 8722 null null 754 505 null null null null null null null null 100 100 null null null null .897 1.115 null null 1.101 null 52 420 1.166 .98 null null null 115 124 149 158 0 11816 634 11182 1.43 null null .7 null .516 null .516
4 1782 975 713 460 1069 515 null null 717 469 null null null null null null null null 67 63 null null null null 2.076 .482 null null .561 null 52 320 .377 .87 null null null 114 122 175 183 0 1250 589 661 .618 null null 1.617 null -.694 null -.694
5 1611 754 717 457 894 297 null null 726 468 null null null null null null null null 56 40 null null null null 3.01 .332 null null .368 null 52 332 .3 .88 null null null 115 123 199 207 0 966 585 381 .426 null null 2.346 null -1.23 null -1.23
6 5955 1404 723 459 5232 945 null null 736 469 null null null null null null null null 100 86 null null null null 5.537 .181 null null .18 null 80 656 .175 .96 null null null 113 124 220 231 0 1800 588 1212 .232 null null 4.317 null -2.11 null -2.11
7 1860 1048 776 494 1084 554 null null 792 504 null null null null null null null null 86 90 null null null null 1.957 .511 null null .815 null 52 332 .33 .76 null null null 115 123 246 254 0 1343 633 710 .655 null null 1.527 null -.61 null -.61
8 2398 1270 753 520 1645 750 null null 774 510 null null null null null null null null 100 83 null null null null 2.193 .456 null null .661 null 12 104 .347 .78 null null null 117 122 273 278 0 1628 666 962 .585 null null 1.71 null -.774 null -.774
9 5369 5493 794 549 4575 4944 null null 802 557 null null null null null null null null 100 100 null null null null .925 1.081 null null 1.085 null 52 332 1.083 .95 null null null 115 123 294 302 0 7042 703 6339 1.386 null null .722 null .47 null .47
10 2386 1462 845 589 1541 873 null null 861 613 null null null null null null null null 100 96 null null null null 1.765 .567 null null .764 null 32 176 .349 .77 null null null 117 123 320 326 0 1874 755 1119 .726 null null 1.377 null -.462 null -.462
11 3329 2202 900 611 2429 1591 null null 911 629 null null null null null null null null 100 100 null null null null 1.527 .655 null null .855 null 32 236 .521 .8 null null null 115 122 343 350 0 2823 783 2040 .84 null null 1.191 null -.252 null -.252
12 6590 971 922 610 5668 361 null null 978 622 null null null null null null null null 98 50 null null null null 15.701 .064 null null .071 null 120 766 .065 .85 null null null 113 125 365 377 0 1244 782 462 .082 null null 12.268 null -3.617 null -3.617
13 2639 2124 865 582 1774 1542 null null 931 592 null null null null null null null null 85 76 null null null null 1.15 .869 null null .823 null 120 750 1.025 .92 null null null 113 125 387 399 0 2723 746 1977 1.114 null null .897 null .156 null .156
14 10924 11015 898 648 10026 10367 null null 923 676 null null null null null null null null 98 96 null null null null .967 1.034 null null .959 null 120 794 1.059 .99 null null null 113 125 411 423 0 14121 830 13291 1.326 null null .754 null .407 null .407
15 3026 1499 924 695 2102 804 null null 924 706 null null null null null null null null 96 76 null null null null 2.614 .382 null null .383 null 52 332 .374 .92 null null null 115 123 439 447 0 1921 891 1030 .49 null null 2.041 null -1.029 null -1.029
16 2993 2764 866 654 2127 2110 null null 874 664 null null null null null null null null 100 98 null null null null 1.008 .992 null null .995 null 80 552 .957 .9 null null null 114 124 460 470 0 3543 838 2705 1.272 null null .786 null .347 null .347
17 5150 5328 846 642 4304 4686 null null 854 652 null null null null null null null null 100 100 null null null null .918 1.089 null null 1.012 null 80 552 1.166 .96 null null null 114 124 484 494 0 6830 823 6007 1.396 null null .716 null .481 null .481
18 4156 4279 843 586 3313 3693 null null 851 601 null null null null null null null null 100 100 null null null null .897 1.115 null null 1.183 null 52 332 1.082 .89 null null null 139 147 102 110 0 5485 751 4734 1.429 null null .7 null .515 null .515
19 6538 4565 851 623 5687 3942 null null 869 635 null null null null null null null null 100 100 null null null null 1.443 .693 null null .702 null 52 340 .701 .92 null null null 139 147 127 135 0 5852 798 5054 .889 null null 1.125 null -.17 null -.17
20 2352 1114 856 610 1496 504 null null 875 636 null null null null null null null null 100 56 null null null null 2.968 .337 null null .365 null 32 176 .306 .81 null null null 140 146 152 158 0 1428 782 646 .432 null null 2.316 null -1.212 null -1.212

Total number of rows: 4608

Table truncated, full table size 1173 Kbytes.




Supplementary data files not provided
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