NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM69983 Query DataSets for GSM69983
Status Public on Aug 16, 2005
Title J99-A5-1 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-A5 genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng J99-A5 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17823.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 12035 11782 803 327 11232 11455 12017 11688 864 398 11214 11361 0 0 9688 10278 270 227 80 85 74 78 22687 22575 .981 1.02 1.013 .876 1.007 3.258 120 810 1.043 .96 120 1170 13290 43 55 31 43 0 13376 371 13004 1.158 13269 12898 .864 1.15 .211 .202
2 11545 1030 790 325 10755 705 11156 800 816 344 10366 475 0 0 3528 488 190 101 100 96 100 92 11460 10841 15.255 .066 .046 .058 .057 1.649 52 340 .067 .85 80 1410 13280 44 52 57 65 0 1169 369 800 .074 908 539 13.438 .052 -3.748 -4.265
3 11437 11075 716 294 10721 10781 10547 11316 740 331 9831 11022 0 0 5621 6063 190 137 100 100 98 97 21502 20853 .994 1.006 1.121 .901 .95 2.071 80 656 1.027 .93 110 1650 13270 41 52 79 90 0 12573 334 12239 1.142 12847 12513 .876 1.273 .191 .348
4 792 359 632 225 160 134 687 228 640 237 55 3 0 0 350 304 140 78 38 30 21 23 294 58 1.194 .838 .055 .477 .438 3.181 80 656 .625 .55 110 1890 13270 41 52 103 114 -100 408 255 152 .951 259 3 1.052 .062 -.073 -4.013
5 910 373 663 241 247 132 668 254 676 257 5 13 0 0 525 275 179 209 33 27 26 17 379 18 1.871 .534 2.6 .451 .45 3.348 80 656 .46 .75 110 2120 13270 41 52 126 137 -100 423 274 150 .607 288 15 1.648 2.952 -.721 1.562
6 11632 4608 724 281 10908 4327 9716 3595 739 282 8992 3314 0 0 7591 3602 170 72 100 100 100 100 15235 12306 2.521 .397 .369 .355 .417 1.622 52 340 .417 .95 80 2370 13270 43 51 153 161 0 5231 319 4912 .45 4081 3762 2.221 .418 -1.151 -1.257
7 1310 686 675 264 635 422 830 337 690 269 155 73 0 0 982 672 155 72 50 50 37 41 1057 228 1.505 .665 .471 .523 .572 2.874 80 656 .617 .82 110 2600 13270 41 52 174 185 -100 779 300 479 .754 383 83 1.325 .535 -.406 -.903
8 1114 546 643 244 471 302 715 280 654 250 72 36 0 0 779 480 151 66 40 46 36 38 773 108 1.56 .641 .5 .699 .678 2.215 80 656 .559 .87 110 2840 13270 41 52 198 209 -100 620 277 343 .728 318 41 1.374 .568 -.458 -.817
9 9952 8322 674 264 9278 8058 7950 7278 683 269 7276 7014 0 0 7669 6534 155 73 100 100 98 98 17336 14290 1.151 .869 .964 .878 .813 1.847 52 420 .846 .96 90 3090 13270 42 51 224 233 0 9448 300 9148 .986 8262 7963 1.014 1.094 -.02 .13
10 2677 1627 689 293 1988 1334 3090 1246 722 301 2401 953 0 0 1279 860 191 90 100 100 100 100 3322 3354 1.49 .671 .397 .739 .709 2.117 12 62 .627 .8 40 3310 13260 44 48 249 253 0 1847 333 1514 .762 1415 1082 1.313 .451 -.393 -1.15
11 2246 1447 669 268 1577 1179 1692 1005 675 269 1023 737 0 0 1355 1025 139 89 93 96 81 84 2756 1760 1.338 .748 .72 .781 .857 2.875 32 170 .723 .87 60 3560 13260 43 49 273 279 0 1643 304 1338 .849 1141 837 1.178 .818 -.237 -.29
12 13672 1036 713 259 12959 777 13705 1008 715 267 12992 749 0 0 2956 274 151 79 100 100 100 100 13736 13741 16.678 .06 .058 .058 .06 1.327 52 332 .058 .92 80 3800 13260 42 50 296 304 0 1176 294 882 .068 1144 850 14.691 .065 -3.877 -3.933
13 4874 5899 670 271 4204 5628 4978 6138 687 270 4308 5867 0 0 1637 2053 143 74 100 100 100 100 9832 10175 .747 1.339 1.362 1.374 1.279 1.62 52 420 1.353 .93 90 4030 13270 42 51 318 327 0 6697 308 6389 1.52 6968 6661 .658 1.546 .604 .629
14 8473 6465 703 284 7770 6181 7704 5714 735 302 7001 5430 0 0 4575 3844 204 110 100 100 100 100 13951 12431 1.257 .795 .776 .795 .835 1.632 52 412 .797 .93 90 4290 13260 41 50 344 353 0 7339 322 7017 .903 6487 6164 1.107 .881 -.147 -.184
15 5561 1010 622 221 4939 789 6221 1063 625 228 5599 842 0 0 2752 553 146 61 100 96 100 84 5728 6441 6.26 .16 .15 .144 .157 2.062 32 170 .157 .89 60 4530 13260 43 49 370 376 0 1147 251 896 .181 1207 956 5.514 .171 -2.463 -2.55
16 2839 1665 580 218 2259 1447 2101 1151 593 226 1521 933 0 0 1618 1205 126 63 100 100 100 100 3706 2454 1.561 .641 .613 .571 .608 1.631 32 230 .663 .92 70 4770 13260 42 49 393 400 0 1890 247 1643 .727 1307 1059 1.375 .696 -.46 -.522
17 2572 3059 575 216 1997 2843 1673 1988 588 218 1098 1772 0 0 2176 2682 130 56 98 100 94 100 4840 2870 .702 1.424 1.614 1.692 1.533 1.779 52 340 1.328 .94 80 5000 13270 43 51 416 424 0 3473 245 3228 1.616 2257 2012 .619 1.832 .693 .874
18 3705 2048 770 324 2935 1724 2457 1328 769 322 1687 1004 0 0 2581 1627 148 76 96 100 96 96 4659 2691 1.702 .587 .595 .544 .631 2.752 32 176 .568 .86 60 1180 13520 69 75 35 41 0 2325 368 1957 .667 1508 1140 1.5 .676 -.585 -.566
19 5043 3445 694 291 4349 3154 4664 3486 728 298 3970 3195 0 0 2491 1955 166 80 100 100 100 100 7503 7165 1.379 .725 .805 .67 .776 1.72 32 236 .727 .92 70 1410 13510 67 74 57 64 0 3911 330 3581 .823 3958 3627 1.215 .914 -.28 -.13
20 825 308 656 271 169 37 794 274 668 275 138 3 0 0 289 171 142 70 46 23 23 15 206 141 4.568 .219 .022 .37 .329 4.315 80 656 .237 .36 110 1650 13510 65 76 79 90 -50 350 308 42 .249 311 3 4.023 .025 -2.008 -5.341

Total number of rows: 4608

Table truncated, full table size 1123 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap