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Sample GSM73600 Query DataSets for GSM73600
Status Public on Sep 09, 2005
Title control 86:2 genomic DNA vs. Tigr/Astra ref
Sample type genomic
 
Channel 1
Source name 1 ug 26695 genomic DNA + 1ug J99 genomic DNA
Organism Helicobacter pylori
Characteristics 1 ug 26695 genomic DNA + 1ug J99 genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug control 86:2 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug control 86:2 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-09/10212.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 6782 7581 3139 3082 3643 4499 null null 3167 3108 null null null null null null null null 92 86 null null null null .81 1.235 null null 1.271 null 80 560 1.224 .93 null null null 86 96 67 77 0 6424 2611 3813 1.047 null null .955 null .066 null .066
2 5938 3030 3319 3245 2619 -215 null null 3321 3263 null null null null null null null null 84 21 null null null null null null null null .38 null 52 340 .179 .43 null null null 85 93 93 101 0 2567 2750 -183 null null null null null null null null
3 6241 6723 3280 3339 2961 3384 null null 3360 3389 null null null null null null null null 88 83 null null null null .875 1.143 null null 1.08 null 80 560 1.108 .92 null null null 85 95 115 125 0 5697 2829 2868 .969 null null 1.032 null -.046 null -.046
4 2569 2693 3577 3552 -1008 -859 null null 3392 3443 null null null null null null null null 6 9 null null null null null null null null 1.018 null 32 236 .885 .85 null null null 84 91 143 150 -100 2282 3010 -728 null null null null null null null
5 944 1035 3967 3733 -3023 -2698 null null 3333 3225 null null null null null null null null 0 0 null null null null null null null null .892 null 32 236 .891 .93 null null null 84 91 167 174 -100 877 3163 -2286 null null null null null null null
6 8487 8898 3768 3550 4719 5348 null null 2687 2710 null null null null null null null null 43 51 null null null null .882 1.133 null null 1.041 null 80 542 1.012 .95 null null null 85 95 183 193 0 7540 3008 4532 .96 null null 1.041 null -.058 null -.058
7 305 400 171 281 134 119 null null 455 810 null null null null null null null null 0 0 null null null null 1.126 .888 null null 1.053 null 12 104 1.07 .91 null null null 85 90 214 219 -100 338 238 100 .746 null null 1.34 null null -.422
8 3801 3717 3286 3311 515 406 null null 2909 3093 null null null null null null null null 33 25 null null null null 1.268 .788 null null 1.147 null 12 104 .856 .8 null null null 85 90 239 244 -100 3150 2805 345 .67 null null 1.493 null null -.578
9 5416 5604 3009 3205 2407 2399 null null 3516 3858 null null null null null null null null 13 11 null null null null 1.003 .997 null null .993 null 52 320 .61 .6 null null null 83 91 261 269 0 4749 2716 2033 .845 null null 1.184 null -.244 null -.244
10 2689 2678 2966 3169 -277 -491 null null 2989 3179 null null null null null null null null 15 18 null null null null null null null null 1.261 null 32 160 .925 .74 null null null 84 90 287 293 -100 2269 2685 -416 null null null null null null null
11 3590 3717 2681 2918 909 799 null null 2701 2891 null null null null null null null null 53 50 null null null null 1.138 .879 null null 1.066 null 32 230 .875 .8 null null null 83 90 309 316 -100 3150 2472 678 .746 null null 1.341 null null -.423
12 5433 2782 2561 2787 2872 -5 null null 2585 2832 null null null null null null null null 95 23 null null null null null null null null .289 null 80 560 .009 .04 null null null 84 94 331 341 0 2357 2361 -4 null null null null null null null null
13 3318 3017 2506 2741 812 276 null null 2535 2741 null null null null null null null null 75 40 null null null null 2.942 .34 null null .735 null 52 332 .613 .69 null null null 84 92 358 366 0 2556 2322 234 .288 null null 3.47 null -1.795 null -1.795
14 8377 11751 2469 2796 5908 8955 null null 2550 2899 null null null null null null null null 96 95 null null null null .66 1.516 null null 1.335 null 80 552 1.585 .96 null null null 83 93 380 390 0 9958 2369 7589 1.285 null null .778 null .361 null .361
15 3235 3046 2710 3013 525 33 null null 2819 3110 null null null null null null null null 43 25 null null null null 15.909 .063 null null 1.028 null 32 236 .659 .69 null null null 86 93 406 413 -100 2581 2553 28 .053 null null 18.75 null null -4.229
16 3487 4067 2624 3058 863 1009 null null 2703 3100 null null null null null null null null 40 37 null null null null .855 1.169 null null 1.661 null 32 160 1.103 .76 null null null 84 90 431 437 0 3446 2591 855 .991 null null 1.009 null -.013 null -.013
17 5523 5967 2335 2676 3188 3291 null null 2366 2706 null null null null null null null null 98 92 null null null null .969 1.032 null null .976 null 52 412 1.057 .88 null null null 82 91 452 461 0 5056 2267 2789 .875 null null 1.143 null -.193 null -.193
18 3938 3670 3319 3137 619 533 null null 2423 2363 null null null null null null null null 26 19 null null null null 1.161 .861 null null .876 null 52 340 .844 .96 null null null 110 118 71 79 -100 3110 2658 452 .73 null null 1.369 null null -.454
19 497 579 3308 3615 -2811 -3036 null null 2678 2793 null null null null null null null null 0 0 null null null null null null null null 1.079 null 32 176 1.049 .95 null null null 112 118 95 101 -100 490 3063 -2573 null null null null null null null
20 1185 1355 1101 993 84 362 null null 2273 2363 null null null null null null null null 6 9 null null null null .232 4.31 null null .813 null 32 236 1.003 .96 null null null 109 116 118 125 -100 1148 841 307 3.655 null null .274 null null 1.87

Total number of rows: 4608

Table truncated, full table size 1172 Kbytes.




Supplementary data files not provided
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