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Sample GSM69992 Query DataSets for GSM69992
Status Public on Aug 16, 2005
Title J99-D1-2 vs Tigr/Astra references (250 ug).
Sample type genomic
 
Channel 1
Source name 250 ng Tigr/Astra genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng Tigr/Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 250 ng J99-D1 genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng J99-D1 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17829.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 Aug 15, 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 (1)
GSE3137 H. pilory diversity in human

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 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
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

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
1 31798 41834 788 351 31010 41483 33527 41602 803 353 32739 41251 0 0 6232 8524 160 78 100 100 100 100 72493 73990 .748 1.338 1.26 1.341 1.329 1.178 52 340 1.349 .96 80 1220 41250 53 61 26 34 0 36076 303 35774 1.154 35876 35574 .867 1.087 .206 .12
2 19735 2435 774 385 18961 2050 14939 2453 792 398 14165 2068 0 0 15887 1642 176 109 100 92 100 80 21011 16233 9.249 .108 .146 .101 .102 1.87 52 420 .092 .9 90 1450 41230 50 59 48 57 0 2100 332 1768 .093 2115 1783 10.725 .126 -3.423 -2.99
3 18970 21981 844 450 18126 21531 21175 23556 853 461 20331 23106 0 0 6011 7816 170 112 100 100 100 100 39657 43437 .842 1.188 1.136 1.179 1.155 1.361 52 420 1.213 .96 90 1690 41230 50 59 72 81 0 18956 388 18568 1.024 20314 19926 .976 .98 .035 -.029
4 1135 776 749 391 386 385 758 413 764 398 9 22 0 0 820 749 156 98 31 37 26 31 771 31 1.003 .997 2.444 .885 .812 3.934 80 656 .885 .85 110 1930 41210 47 58 95 106 -100 669 337 332 .86 356 19 1.163 2.108 -.217 1.076
5 1266 752 745 376 521 376 772 388 759 384 27 12 0 0 1013 723 157 95 37 41 31 31 897 39 1.386 .722 .444 .511 .576 2.806 80 656 .68 .88 110 2170 41210 47 58 119 130 -100 649 324 324 .622 335 10 1.607 .383 -.684 -1.384
6 16261 10361 758 343 15503 10018 15938 9911 778 359 15180 9568 0 0 10880 7550 164 94 100 100 100 100 25521 24748 1.548 .646 .63 .603 .632 1.826 52 420 .651 .94 90 2410 41220 49 58 144 153 0 8935 296 8639 .557 8547 8251 1.794 .544 -.844 -.88
7 1299 924 730 322 569 602 837 392 734 328 107 70 0 0 1081 1139 148 82 45 48 38 37 1171 177 .945 1.058 .654 .751 .724 4.202 80 656 1.031 .89 110 2650 41210 47 58 167 178 -100 797 278 519 .912 338 60 1.096 .564 -.132 -.826
8 1343 746 714 300 629 446 906 398 725 308 192 98 0 0 865 677 143 71 57 57 45 45 1075 290 1.41 .709 .51 .668 .696 2.931 80 656 .724 .9 110 2890 41210 47 58 191 202 -100 643 259 385 .611 343 85 1.635 .44 -.71 -1.184
9 11879 13390 719 305 11160 13085 9772 12065 730 323 9053 11760 0 0 8086 10130 141 122 98 100 98 98 24245 20813 .853 1.172 1.299 1.075 1.06 1.869 52 336 1.217 .96 80 3140 41210 49 57 218 226 0 11547 263 11284 1.011 10404 10141 .989 1.12 .016 .164
10 2995 2919 734 321 2261 2598 2635 2951 738 347 1901 2630 0 0 1535 1731 154 117 100 100 100 100 4859 4531 .87 1.149 1.383 1.08 1.156 2.043 12 104 1.148 .89 50 3380 41210 50 55 243 248 0 2517 277 2240 .991 2545 2268 1.009 1.193 -.013 .255
11 3762 3254 791 338 2971 2916 3809 3173 818 356 3018 2835 0 0 1145 1793 175 114 100 100 100 100 5887 5853 1.019 .981 .939 .828 .966 1.892 12 98 1.072 .89 50 3600 41200 49 54 265 270 0 2806 291 2515 .846 2736 2445 1.181 .81 -.241 -.304
12 18465 2122 843 393 17622 1729 18998 2093 858 405 18155 1700 0 0 3952 525 157 90 100 100 100 100 19351 19855 10.192 .098 .094 .095 .099 1.27 52 420 .097 .95 90 3850 41220 49 58 288 297 0 1830 339 1491 .085 1805 1466 11.819 .081 -3.563 -3.63
13 5631 10408 902 489 4729 9919 5453 10744 912 494 4551 10255 0 0 1649 3569 172 128 100 100 100 100 14648 14806 .477 2.097 2.253 2.074 2.114 1.31 52 340 2.212 .95 80 4090 41210 49 57 313 321 0 8976 422 8554 1.809 9265 8844 .553 1.943 .855 .958
14 13502 12915 1031 638 12471 12277 12946 13148 1029 645 11915 12510 0 0 4188 5377 179 148 100 100 100 100 24748 24425 1.016 .984 1.05 .911 .996 1.444 52 340 1.038 .95 80 4330 41210 49 57 337 345 0 11138 550 10587 .849 11338 10788 1.178 .905 -.236 -.143
15 10030 2887 864 487 9166 2400 10511 2851 896 469 9647 2364 0 0 1986 738 191 127 100 100 100 100 11566 12011 3.819 .262 .245 .255 .245 1.364 12 98 .264 .92 50 4590 41200 49 54 364 369 0 2490 420 2070 .226 2459 2039 4.429 .211 -2.147 -2.242
16 5702 4522 747 399 4955 4123 5616 4466 788 437 4869 4067 0 0 2671 2444 184 139 100 100 100 100 9078 8936 1.202 .832 .835 .783 .844 1.481 12 90 .882 .95 50 4810 41190 48 53 386 391 0 3900 344 3556 .718 3851 3507 1.394 .72 -.479 -.473
17 2587 3646 770 453 1817 3193 1756 2146 774 456 986 1693 0 0 1942 3555 146 97 100 100 96 100 5010 2679 .569 1.757 1.717 1.775 1.793 1.548 52 340 1.879 .92 80 5060 41210 49 57 410 418 0 3144 391 2754 1.515 1851 1460 .66 1.481 .6 .566
18 5400 4445 734 315 4666 4130 4520 2692 744 325 3786 2377 0 0 4069 3691 145 75 100 96 96 93 8796 6163 1.13 .885 .628 .966 1.034 1.987 32 176 .889 .93 60 1230 41450 74 80 28 34 0 3833 272 3562 .763 2321 2050 1.31 .541 -.39 -.885
19 5894 5350 727 325 5167 5025 4952 3773 738 329 4225 3448 0 0 3704 4379 144 94 98 100 98 100 10192 7673 1.028 .973 .816 .951 .885 1.687 52 340 1.069 .94 80 1460 41460 74 82 50 58 0 4614 280 4333 .839 3254 2973 1.192 .704 -.254 -.507
20 938 481 750 370 188 111 813 365 756 377 63 -5 0 0 497 381 147 80 33 27 21 15 299 58 1.694 .59 null .621 .668 4.122 80 656 .614 .72 110 1690 41450 71 82 71 82 -50 415 319 96 .509 315 -4 1.964 null -.974 null

Total number of rows: 4608

Table truncated, full table size 1118 Kbytes.




Supplementary data files not provided
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