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Sample GSM184247 Query DataSets for GSM184247
Status Public on Aug 09, 2007
Title 259a1 rep2
Sample type genomic
 
Channel 1
Source name 0.25 ug Tigr/Astra Reference
Organism Helicobacter pylori
Characteristics 0.25 ug Tigr/Astra Reference
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.25 ug 259a1
Organism Helicobacter pylori
Characteristics 0.25 ug 259a1
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32399.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Apr 25, 2007
Last update date Aug 08, 2007
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)
GSE7618 Array CGH of Mexican Patient Isolates and BCS100 Strain

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 3273 4309 268 247 3005 4062 492 870 455 405 224 623 0 0 4365 5596 478 438 46 51 44 48 7067 847 .74 1.352 2.781 1.549 1.36 2.356 52 312 1.289 .99 80 1910 11930 109 117 123 131 0 3882 223 3659 1.218 784 561 .821 2.506 .284 1.325
2 6390 2690 916 696 5474 1994 5527 1988 1049 940 4611 1292 0 0 4200 2228 983 1334 82 48 82 28 7468 5903 2.745 .364 .28 .269 .291 2.63 52 332 .468 .83 80 2150 11930 109 117 147 155 0 2423 627 1796 .328 1791 1164 3.047 .252 -1.607 -1.986
3 8756 10064 904 720 7852 9344 6726 7046 1472 882 5822 6326 0 0 6323 7652 5004 1430 53 84 38 76 17196 12148 .84 1.19 1.087 1.191 1.17 1.2 52 332 1.181 .97 80 2390 11930 109 117 171 179 0 9067 649 8418 1.072 6348 5699 .933 .979 .1 -.031
4 1697 2056 976 875 721 1181 1054 1039 1068 933 78 164 0 0 1358 2123 1436 487 19 42 7 32 1902 242 .61 1.638 2.103 1.422 1.544 1.929 52 412 1.572 .98 90 2640 11930 108 117 195 204 0 1852 788 1064 1.476 936 148 .678 1.894 .561 .922
5 1658 2139 1109 1122 549 1017 870 846 1168 1230 -239 -276 0 0 1409 2297 262 357 32 36 32 32 1566 -515 .54 1.852 null 1.402 1.408 1.839 52 412 1.648 .97 90 2880 11930 108 117 219 228 0 1927 1011 916 1.669 762 null .599 null .739 null
6 15597 7736 1298 1415 14299 6321 12725 5693 2438 2738 11427 4278 0 0 11059 5844 7709 8077 57 34 40 7 20620 15705 2.262 .442 .374 .318 .362 1.794 52 412 .808 .91 90 3120 11930 108 117 243 252 0 6969 1275 5695 .398 5129 3854 2.511 .337 -1.328 -1.568
7 1871 2228 912 784 959 1444 1446 1581 930 802 534 797 0 0 1094 1644 189 277 69 61 55 53 2403 1331 .664 1.506 1.493 1.31 1.383 1.786 52 400 1.518 .97 90 3360 11920 107 116 267 276 0 2007 706 1301 1.357 1424 718 .737 1.345 .44 .427
8 1663 1906 867 664 796 1242 950 857 889 706 83 193 0 0 1279 1848 175 225 42 48 40 44 2038 276 .641 1.56 2.325 1.493 1.384 2.378 52 400 1.462 .97 90 3600 11920 107 116 291 300 0 1717 598 1119 1.406 772 174 .711 2.095 .491 1.067
9 4177 5353 773 477 3404 4876 3883 4766 787 501 3110 4289 0 0 2817 3986 185 155 92 96 92 92 8280 7399 .698 1.432 1.379 1.394 1.417 1.191 52 394 1.409 .99 90 3840 11920 107 116 315 324 0 4823 430 4393 1.29 4294 3864 .775 1.242 .368 .313
10 2345 3365 765 469 1580 2896 1439 2267 795 510 674 1798 0 0 1951 3301 400 244 63 76 46 65 4476 2472 .546 1.833 2.668 1.921 1.877 2.376 52 400 1.745 .98 90 4080 11930 108 117 339 348 0 3032 423 2609 1.651 2042 1620 .606 2.403 .724 1.265
11 1478 1697 806 540 672 1157 1295 1388 862 610 489 848 0 0 640 1027 273 367 65 71 44 51 1829 1337 .581 1.722 1.734 1.894 1.78 2.012 52 400 1.647 .94 90 4320 11930 108 117 363 372 0 1529 486 1042 1.551 1250 764 .645 1.562 .633 .644
12 6558 6231 734 433 5824 5798 5070 5327 773 520 4336 4894 0 0 5214 4628 251 371 98 98 98 98 11622 9230 1.004 .996 1.129 1.032 1.027 1.151 52 400 .941 .99 90 4560 11930 108 117 387 396 0 5614 390 5223 .897 4799 4409 1.115 1.017 -.157 .024
13 2786 3170 795 538 1991 2632 2158 2117 810 584 1363 1579 0 0 1839 2507 193 192 92 100 80 88 4623 2942 .756 1.322 1.158 1.434 1.33 1.563 52 306 1.336 .98 80 4790 11930 109 117 411 419 0 2856 485 2371 1.191 1907 1423 .84 1.044 .252 .062
14 6483 9790 744 508 5739 9282 7043 11616 822 597 6299 11108 0 0 3936 6287 799 855 82 88 75 80 15021 17407 .618 1.617 1.763 1.664 1.605 1.148 52 306 1.584 .99 80 5030 11930 109 117 435 443 0 8820 458 8362 1.457 10465 10007 .686 1.589 .543 .668
15 2825 3764 752 555 2073 3209 2089 2503 759 568 1337 1948 0 0 2287 3544 119 137 80 82 76 78 5282 3285 .646 1.548 1.457 1.275 1.531 1.823 52 306 1.549 .99 80 5270 11930 109 117 459 467 0 3391 500 2891 1.395 2255 1755 .717 1.313 .48 .392
16 1606 1914 846 676 760 1238 1133 1037 866 706 287 361 0 0 1185 1886 177 194 57 58 46 48 1998 648 .614 1.629 1.258 1.397 1.625 1.874 80 552 1.599 .98 100 5530 11950 110 120 484 494 0 1724 609 1115 1.468 934 325 .681 1.133 .553 .18
17 2204 2410 821 641 1383 1769 1532 1388 838 666 711 747 0 0 1830 2402 192 167 71 76 65 63 3152 1458 .782 1.279 1.051 1.275 1.218 1.853 80 552 1.304 .99 100 5770 11950 110 120 508 518 0 2171 577 1594 1.152 1250 673 .868 .947 .205 -.079
18 518 504 274 256 244 248 268 271 542 499 -6 15 0 0 787 706 524 502 7 11 7 7 492 9 .984 1.016 null 1.034 .955 2.125 52 332 .96 .96 80 1920 12140 130 138 124 132 0 454 231 223 .916 244 14 1.092 null -.127 null
19 6595 6894 939 748 5656 6146 5232 5649 1049 877 4293 4901 0 0 4480 4934 933 742 84 86 78 82 11802 9194 .92 1.087 1.142 .989 1.038 1.476 52 340 1.083 .98 80 2160 12150 131 139 148 156 0 6211 674 5537 .979 5089 4415 1.022 1.028 -.031 .041
20 2097 2070 920 752 1177 1318 912 675 971 838 -8 -77 0 0 1848 2359 294 430 44 40 42 38 2495 -85 .893 1.12 null 1.848 1.395 2.376 52 340 1.324 .98 80 2400 12150 131 139 172 180 0 1865 677 1187 1.009 608 null .991 null .013 null

Total number of rows: 4608

Table truncated, full table size 1109 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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