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Sample GSM73599 Query DataSets for GSM73599
Status Public on Sep 09, 2005
Title Hp1 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 Hp1 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug Hp1 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-10/10881.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 10961 6402 553 678 10408 5724 null null 781 897 null null null null null null null null 82 71 null null null null 1.818 .55 null null .505 null 52 420 .581 .91 null null null 112 121 71 80 0 9278 982 8296 .797 null null 1.255 null -.327 null -.327
2 4757 1256 543 607 4214 649 null null 601 667 null null null null null null null null 100 59 null null null null 6.493 .154 null null .167 null 32 230 .128 .73 null null null 112 119 98 105 0 1820 879 941 .223 null null 4.478 null -2.163 null -2.163
3 7679 5820 525 633 7154 5187 null null 559 686 null null null null null null null null 100 88 null null null null 1.379 .725 null null .711 null 52 320 .734 .96 null null null 112 120 121 129 0 8434 917 7517 1.051 null null .952 null .071 null .071
4 1626 1240 487 597 1139 643 null null 504 636 null null null null null null null null 87 53 null null null null 1.771 .565 null null .681 null 32 236 .556 .82 null null null 113 120 147 154 0 1797 865 932 .818 null null 1.222 null -.289 null -.289
5 1792 1599 522 589 1270 1010 null null 720 812 null null null null null null null null 37 28 null null null null 1.257 .795 null null .78 null 32 236 .79 .89 null null null 113 120 172 179 0 2317 853 1464 1.153 null null .867 null .205 null .205
6 6771 1591 508 647 6263 944 null null 685 979 null null null null null null null null 75 5 null null null null 6.635 .151 null null .138 null 52 320 .151 .67 null null null 112 120 195 203 0 2305 937 1368 .218 null null 4.578 null -2.195 null -2.195
7 3003 2279 521 604 2482 1675 null null 524 641 null null null null null null null null 100 91 null null null null 1.482 .675 null null .662 null 12 104 .528 .87 null null null 114 119 220 225 0 3302 875 2427 .978 null null 1.023 null -.032 null -.032
8 2145 1472 523 686 1622 786 null null 530 705 null null null null null null null null 100 66 null null null null 2.064 .485 null null .502 null 12 104 .509 .84 null null null 114 119 246 251 0 2133 994 1139 .702 null null 1.424 null -.51 null -.51
9 6722 5079 565 658 6157 4421 null null 568 685 null null null null null null null null 100 96 null null null null 1.393 .718 null null .699 null 52 320 .708 .95 null null null 112 120 268 276 0 7360 953 6407 1.041 null null .961 null .057 null .057
10 2643 2146 562 682 2081 1464 null null 580 707 null null null null null null null null 93 75 null null null null 1.421 .704 null null .797 null 32 170 .539 .83 null null null 114 120 294 300 0 3110 988 2122 1.02 null null .981 null .028 null .028
11 2212 1954 584 683 1628 1271 null null 593 726 null null null null null null null null 92 82 null null null null 1.281 .781 null null .802 null 52 420 .719 .9 null null null 112 121 314 323 0 2831 989 1842 1.131 null null .884 null .178 null .178
12 8491 1660 614 694 7877 966 null null 621 718 null null null null null null null null 100 57 null null null null 8.154 .123 null null .079 null 80 560 .111 .56 null null null 113 123 339 349 0 2405 1005 1400 .178 null null 5.626 null -2.492 null -2.492
13 4994 3895 632 738 4362 3157 null null 641 771 null null null null null null null null 100 100 null null null null 1.382 .724 null null .702 null 52 420 .719 .93 null null null 112 121 363 372 0 5644 1069 4575 1.049 null null .953 null .069 null .069
14 12480 11460 605 725 11875 10735 null null 609 754 null null null null null null null null 100 100 null null null null 1.106 .904 null null .906 null 80 552 .88 .97 null null null 112 122 386 396 0 16608 1050 15558 1.31 null null .763 null .39 null .39
15 3698 3299 561 693 3137 2606 null null 564 712 null null null null null null null null 98 92 null null null null 1.204 .831 null null .854 null 52 332 .796 .94 null null null 113 121 412 420 0 4781 1004 3777 1.204 null null .831 null .268 null .268
16 3738 3300 551 728 3187 2572 null null 595 814 null null null null null null null null 98 71 null null null null 1.239 .807 null null .83 null 52 420 .88 .81 null null null 112 121 435 444 0 4782 1055 3727 1.169 null null .855 null .226 null .226
17 5024 5006 532 704 4492 4302 null null 535 731 null null null null null null null null 100 96 null null null null 1.044 .958 null null .946 null 80 552 .948 .96 null null null 112 122 459 469 0 7255 1020 6235 1.388 null null .72 null .473 null .473
18 5548 3212 687 756 4861 2456 null null 831 974 null null null null null null null null 78 40 null null null null 1.979 .505 null null .506 null 32 236 .493 .96 null null null 137 144 77 84 0 4655 1095 3560 .732 null null 1.365 null -.449 null -.449
19 7235 5684 739 783 6496 4901 null null 793 843 null null null null null null null null 100 100 null null null null 1.325 .754 null null .785 null 32 236 .756 .97 null null null 137 144 100 107 0 8237 1134 7103 1.093 null null .915 null .129 null .129
20 2075 1280 637 711 1438 569 null null 787 884 null null null null null null null null 62 31 null null null null 2.527 .396 null null .509 null 32 236 .64 .88 null null null 137 144 125 132 0 1855 1030 825 .574 null null 1.743 null -.802 null -.802

Total number of rows: 4608

Table truncated, full table size 1163 Kbytes.




Supplementary data files not provided
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