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Sample GSM69981 Query DataSets for GSM69981
Status Public on Aug 16, 2005
Title J99-Cardia 1-1 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-Cardia 1 genomic DNA
Organism Helicobacter pylori
Characteristics 250 ng J99-Cardia 1 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17821.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 31322 23999 1026 295 30296 23704 35256 25342 1056 310 34230 25047 0 0 13560 11624 222 111 100 98 100 98 54000 59277 1.278 .782 .732 .729 .769 1.552 80 560 .794 .97 100 980 12640 43 53 29 39 0 28273 348 27926 .922 29855 29508 1.085 .862 -.118 -.214
2 13678 884 1045 287 12633 597 7089 506 1069 302 6044 219 0 0 13846 746 236 107 96 63 93 50 13230 6263 21.161 .047 .036 .057 .048 2.319 80 560 .047 .91 100 1220 12640 43 53 53 63 0 1041 338 703 .056 596 258 17.962 .043 -4.167 -4.55
3 22887 20615 1005 282 21882 20333 23843 19821 1042 295 22838 19539 0 0 7112 8998 238 99 100 100 100 100 42215 42377 1.076 .929 .856 .869 .9 1.448 52 420 .956 .96 90 1460 12630 42 51 77 86 0 24286 332 23954 1.095 23351 23019 .913 1.008 .131 .011
4 1085 364 965 254 120 110 965 259 979 261 0 5 0 0 481 299 185 68 22 30 15 17 230 5 1.091 .917 null .411 .483 4.124 80 656 .428 .66 110 1690 12620 40 51 99 110 -100 429 299 130 1.08 305 6 .926 null .111 null
5 1737 479 944 253 793 226 1693 445 979 258 749 192 0 0 377 132 251 64 91 100 83 58 1019 941 3.509 .285 .256 .277 .241 2.323 12 98 .204 .6 50 1960 12610 42 47 129 134 -100 564 298 266 .336 524 226 2.978 .302 -1.575 -1.727
6 13481 5685 913 246 12568 5439 7849 3279 932 251 6936 3033 0 0 11014 5359 197 59 100 100 100 100 18007 9969 2.311 .433 .437 .384 .429 1.594 52 332 .45 .96 80 2170 12620 42 50 149 157 0 6697 290 6408 .51 3863 3573 1.961 .515 -.972 -.957
7 2860 1698 844 230 2016 1468 3106 1913 853 240 2262 1683 0 0 853 693 179 67 100 100 100 100 3484 3945 1.373 .728 .744 .7 .714 1.341 12 62 .64 .86 40 2420 12620 44 48 176 180 -100 2000 271 1729 .858 2254 1983 1.166 .877 -.221 -.19
8 2452 937 857 224 1595 713 2468 901 878 226 1611 677 0 0 380 215 179 53 100 100 100 100 2308 2288 2.237 .447 .42 .432 .436 1.379 12 90 .421 .88 50 2670 12600 41 46 200 205 -100 1104 264 840 .527 1061 798 1.899 .495 -.925 -1.014
9 13003 11026 900 232 12103 10794 10132 7317 898 244 9232 7085 0 0 9642 9526 169 71 98 100 98 100 22897 16317 1.121 .892 .767 .79 .846 1.74 52 412 .935 .97 90 2910 12610 40 49 222 231 0 12990 273 12716 1.051 8620 8347 .952 .904 .071 -.145
10 1837 1006 857 233 980 773 1750 1036 872 238 893 803 0 0 480 312 149 65 91 100 91 100 1753 1696 1.268 .789 .899 .713 .681 1.472 12 54 .615 .81 40 3150 12610 43 47 249 253 0 1185 274 911 .929 1221 946 1.076 1.059 -.106 .083
11 2547 1362 843 222 1704 1140 2671 1413 850 233 1828 1191 0 0 550 423 183 70 100 100 100 100 2844 3019 1.495 .669 .652 .651 .687 1.227 12 98 .65 .93 50 3380 12610 42 47 271 276 0 1605 262 1343 .788 1665 1403 1.269 .768 -.343 -.382
12 14196 762 933 229 13263 533 14436 771 944 233 13503 542 0 0 3142 182 180 59 100 100 100 100 13796 14045 24.884 .04 .04 .039 .038 1.389 52 420 .039 .92 90 3620 12620 41 50 293 302 0 898 270 628 .047 908 639 21.122 .047 -4.401 -4.402
13 5726 7480 958 268 4768 7212 6059 7956 979 282 5101 7688 0 0 1486 2528 173 101 100 100 100 100 11980 12789 .661 1.513 1.507 1.49 1.519 1.375 32 236 1.553 .95 70 3850 12630 43 50 317 324 0 8812 316 8496 1.782 9373 9057 .561 1.776 .833 .828
14 10610 7443 994 296 9616 7147 9305 5273 1010 313 8311 4977 0 0 5275 4993 200 101 100 100 100 100 16763 13288 1.345 .743 .599 .674 .72 1.345 52 412 .796 .96 90 4110 12610 40 49 342 351 0 8769 349 8420 .876 6212 5863 1.142 .705 -.192 -.503
15 9438 1554 979 284 8459 1270 9050 1536 1008 293 8071 1252 0 0 2221 533 242 76 100 100 100 100 9729 9323 6.661 .15 .155 .141 .148 1.312 12 98 .159 .96 50 4360 12610 42 47 369 374 0 1831 335 1496 .177 1810 1475 5.654 .183 -2.499 -2.452
16 5646 3126 968 273 4678 2853 5909 3151 1005 300 4941 2878 0 0 1827 1448 209 124 100 100 100 100 7531 7819 1.64 .61 .582 .577 .602 1.281 12 98 .641 .96 50 4590 12610 42 47 392 397 0 3683 322 3361 .718 3712 3391 1.392 .686 -.477 -.543
17 4198 4456 994 308 3204 4148 2904 2526 1000 334 1910 2218 0 0 2899 4268 181 119 100 100 100 100 7352 4128 .772 1.295 1.161 1.205 1.245 1.394 32 170 1.388 .97 60 4830 12620 43 49 416 422 0 5250 363 4887 1.525 2976 2613 .656 1.368 .609 .452
18 10363 5369 996 253 9367 5116 9326 4237 1027 279 8330 3984 0 0 5867 4609 288 141 100 100 100 91 14483 12314 1.831 .546 .478 .4 .553 2.888 12 104 .61 .92 50 980 12860 67 72 31 36 0 6325 298 6027 .643 4992 4694 1.554 .563 -.636 -.828
19 9774 5591 972 261 8802 5330 9431 3862 974 264 8459 3601 0 0 5563 4476 192 67 100 100 100 100 14132 12060 1.651 .606 .426 .521 .577 1.795 32 236 .658 .92 70 1210 12870 67 74 53 60 0 6587 307 6279 .713 4550 4242 1.402 .502 -.487 -.996
20 2232 809 928 246 1304 563 2200 777 968 255 1272 531 0 0 507 174 199 70 100 100 100 100 1867 1803 2.316 .432 .417 .451 .463 1.333 12 68 .392 .87 40 1460 12860 68 72 80 84 0 953 290 663 .509 915 626 1.966 .492 -.975 -1.024

Total number of rows: 4608

Table truncated, full table size 1124 Kbytes.




Supplementary data files not provided
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