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Sample GSM229024 Query DataSets for GSM229024
Status Public on Feb 24, 2012
Title shgc149|PR00295 Marmoset
Sample type genomic
 
Channel 1
Source name Normal human male genomic DNA
Organism Homo sapiens
Characteristics Normal human male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Marmoset genomic DNA
Organism Callithrix sp.
Characteristics Marmoset genomic DNA
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: Comparative genomics, aCGH cell line
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 Sep 12, 2007
Last update date Feb 24, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL5845
Series (1)
GSE9028 Extended Primate aCGH

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 1427 891 172 257 1255 634 1331 799 179 280 1159 542 0 0 391 544 66 175 100 81 100 69 1889 1701 1.979 .505 .468 .53 .52 .33 64 415 .64 .94 90 2350 6590 46 55 38 47 0 1005 290 715 .57 901 611 1.755 .528 -.811 -.923
2 2145 1875 176 250 1969 1625 2050 1803 185 286 1874 1553 0 0 723 1022 67 190 100 98 100 98 3594 3427 1.212 .825 .829 .78 .83 .31 44 372 .9 .98 70 2500 6600 48 55 54 61 0 2115 282 1833 .931 2034 1752 1.074 .935 -.103 -.097
3 2327 1212 175 251 2152 961 2062 1104 181 281 1887 853 0 0 944 625 65 179 100 94 100 85 3113 2740 2.239 .447 .452 .44 .43 .21 52 373 .53 .98 80 2640 6600 48 56 68 76 0 1367 283 1084 .504 1245 962 1.985 .51 -.989 -.972
4 2094 1548 166 267 1928 1281 2143 1526 175 291 1977 1259 0 0 731 712 62 178 100 98 100 93 3209 3236 1.505 .664 .637 .67 .67 .29 60 384 .75 .98 80 2790 6590 47 55 83 91 0 1746 301 1445 .749 1721 1420 1.334 .718 -.416 -.477
5 1091 1313 173 280 918 1033 1107 1270 180 315 934 990 0 0 236 443 62 190 100 100 100 96 1951 1924 .889 1.125 1.06 1.14 1.06 .49 52 370 1.23 .98 80 2920 6600 48 56 96 104 0 1481 316 1165 1.269 1433 1117 .788 1.196 .344 .258
6 2063 1584 175 263 1888 1321 2022 1427 183 313 1847 1164 0 0 722 693 66 226 100 98 100 90 3209 3011 1.429 .7 .63 .69 .69 .25 52 368 .78 .98 80 3090 6600 48 56 113 121 0 1787 297 1490 .789 1610 1313 1.267 .711 -.341 -.492
7 1616 1892 173 269 1443 1623 1607 1852 178 317 1434 1583 0 0 358 527 63 240 100 100 100 100 3066 3017 .889 1.125 1.104 1.16 1.1 .43 70 305 1.17 .98 90 3220 6600 47 56 125 134 0 2134 303 1831 1.269 2089 1786 .788 1.245 .343 .316
8 1879 2285 169 280 1710 2005 1891 2049 174 316 1722 1769 0 0 577 972 62 191 100 100 100 99 3715 3491 .853 1.173 1.027 1.18 1.18 .45 69 312 1.22 .99 90 3350 6600 47 56 138 147 0 2577 316 2262 1.323 2311 1995 .756 1.159 .403 .213
9 1568 1675 168 277 1400 1398 1569 1592 176 305 1401 1315 0 0 225 520 60 180 100 99 100 99 2798 2716 1.001 .999 .939 1.02 .95 .38 70 308 1.07 .99 90 3500 6600 47 56 153 162 0 1889 312 1577 1.126 1796 1483 .888 1.059 .172 .082
10 2839 3011 166 285 2673 2726 2817 3017 174 315 2651 2732 0 0 618 747 56 191 100 100 100 100 5399 5383 .981 1.02 1.031 1.04 1.02 .3 80 280 1.06 .99 100 3640 6600 47 57 167 177 0 3396 321 3075 1.15 3403 3082 .869 1.162 .202 .217
11 1210 1313 172 267 1038 1046 1208 1263 178 305 1036 996 0 0 230 477 66 190 100 98 100 94 2084 2032 .992 1.008 .961 1.05 1.01 .5 80 328 1.11 .98 100 3790 6600 47 57 182 192 0 1481 301 1180 1.137 1425 1123 .88 1.084 .185 .117
12 1749 1784 169 286 1580 1498 1728 1609 179 336 1559 1323 0 0 352 569 74 241 100 100 100 100 3078 2882 1.055 .948 .849 .95 .96 .33 60 362 1.04 .98 80 3940 6600 48 56 198 206 0 2012 323 1690 1.069 1815 1492 .935 .957 .097 -.063
13 2646 3095 175 283 2471 2812 2611 3042 181 324 2436 2759 0 0 428 780 63 205 100 100 100 100 5283 5195 .879 1.138 1.133 1.14 1.15 .32 70 339 1.19 .99 90 4080 6600 47 56 211 220 0 3491 319 3172 1.284 3431 3112 .779 1.278 .36 .353
14 2485 3060 177 283 2308 2777 2555 3061 185 315 2378 2778 0 0 613 928 63 200 100 100 100 100 5085 5156 .831 1.203 1.168 1.24 1.19 .46 80 329 1.23 .99 100 4240 6600 47 57 227 237 0 3452 319 3132 1.357 3453 3134 .737 1.318 .441 .398
15 1353 1399 176 286 1177 1113 1323 1402 183 310 1147 1116 0 0 246 435 68 190 100 100 100 95 2290 2263 1.058 .946 .973 .95 .97 .36 60 335 1.05 .98 80 4380 6600 48 56 242 250 0 1578 323 1255 1.067 1581 1259 .938 1.098 .093 .134
16 6695 9592 183 296 6512 9296 6290 8778 207 333 6107 8482 0 0 2278 3443 151 229 100 100 100 100 15808 14589 .701 1.428 1.389 1.44 1.41 .34 80 334 1.45 .99 100 4540 6600 47 57 257 267 0 10820 334 10486 1.61 9902 9568 .621 1.567 .687 .648
17 2222 2228 184 313 2038 1915 2195 2195 200 365 2011 1882 0 0 405 581 84 232 100 100 100 100 3953 3893 1.064 .94 .936 .93 .96 .24 80 276 1.02 .99 100 4690 6600 47 57 272 282 0 2513 353 2160 1.06 2476 2123 .943 1.056 .084 .078
18 2905 3901 188 310 2717 3591 3046 3928 204 372 2858 3618 0 0 680 957 93 254 100 99 100 99 6308 6476 .757 1.322 1.266 1.44 1.28 .86 80 278 1.34 .99 100 4830 6600 47 57 286 296 0 4400 350 4051 1.491 4431 4081 .671 1.428 .576 .514
19 6526 5611 194 311 6332 5300 6422 5402 213 362 6228 5091 0 0 1146 1345 95 239 100 100 100 100 11632 11319 1.195 .837 .817 .84 .83 .2 86 294 .86 .99 100 4970 6600 47 57 300 310 0 6329 351 5978 .944 6093 5743 1.059 .922 -.083 -.117
20 1659 1728 190 307 1469 1421 1663 1686 204 334 1473 1379 0 0 267 546 86 194 100 100 100 98 2890 2852 1.034 .967 .936 .97 .93 .39 80 299 1.06 .98 100 5130 6610 48 58 316 326 0 1949 346 1603 1.091 1902 1556 .916 1.056 .126 .079

Total number of rows: 41472

Table truncated, full table size 9394 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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