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Sample GSM229014 Query DataSets for GSM229014
Status Public on Feb 24, 2012
Title shgc152|PR00495 Gibbon
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 Gibbon genomic DNA
Organism Hylobates sp.
Characteristics Gibbon 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 1928 1097 193 211 1735 886 1935 954 197 237 1742 743 0 0 504 554 64 152 100 94 100 87 2621 2485 1.958 .511 .427 .51 .45 .3 69 435 .58 .97 90 2420 5910 42 51 45 54 0 1322 254 1068 .615 1149 895 1.625 .514 -.701 -.96
2 2529 1654 206 233 2323 1421 2556 1671 207 257 2350 1438 0 0 681 642 67 153 100 97 100 97 3744 3788 1.635 .612 .612 .6 .63 .23 60 359 .67 .99 80 2580 5920 44 52 62 70 0 1993 281 1712 .737 2013 1733 1.357 .737 -.44 -.44
3 3001 2159 206 235 2795 1924 3083 2034 207 261 2877 1799 0 0 833 816 70 167 100 100 100 100 4719 4676 1.453 .688 .625 .69 .68 .24 60 362 .73 .98 80 2710 5920 44 52 75 83 0 2601 283 2318 .829 2451 2168 1.206 .753 -.27 -.408
4 2912 1888 207 227 2705 1661 2884 1666 213 258 2677 1439 0 0 816 1064 73 168 100 98 100 93 4366 4116 1.629 .614 .538 .57 .56 .26 44 383 .65 .96 70 2860 5920 44 51 90 97 0 2275 274 2001 .74 2007 1734 1.352 .648 -.435 -.627
5 1605 1155 204 231 1401 924 1630 1137 212 259 1426 906 0 0 347 444 70 166 100 100 100 92 2325 2332 1.516 .66 .635 .7 .68 .39 60 377 .73 .97 80 2990 5920 44 52 103 111 0 1392 278 1113 .795 1370 1092 1.258 .766 -.332 -.386
6 3019 1638 205 244 2814 1394 3048 1495 214 269 2843 1251 0 0 888 824 72 155 100 100 100 98 4208 4094 2.019 .495 .44 .46 .48 .18 44 415 .55 .98 70 3160 5920 44 51 120 127 0 1974 294 1680 .597 1801 1507 1.675 .53 -.745 -.915
7 2404 1371 209 235 2195 1136 2378 1434 213 262 2169 1199 0 0 505 485 69 158 100 99 100 91 3331 3368 1.932 .518 .553 .51 .53 .2 70 312 .58 .98 90 3300 5920 43 52 133 142 0 1652 283 1369 .624 1728 1445 1.604 .666 -.681 -.586
8 2682 1980 204 235 2478 1745 2686 1696 210 271 2482 1461 0 0 761 1002 73 172 100 99 100 99 4223 3943 1.42 .704 .589 .69 .68 .27 69 303 .75 .98 90 3420 5920 43 52 145 154 0 2386 283 2102 .848 2043 1760 1.179 .709 -.237 -.496
9 1887 5446 197 221 1690 5225 1897 5361 203 253 1700 5140 0 0 452 1185 71 160 99 100 98 100 6915 6840 .323 3.092 3.024 3.43 3.03 2.31 80 278 2.84 .99 100 3570 5930 44 54 160 170 0 6562 266 6295 3.725 6459 6193 .268 3.643 1.897 1.865
10 3765 5921 188 221 3577 5700 3675 5242 197 241 3487 5021 0 0 718 2450 72 148 100 100 100 100 9277 8508 .628 1.594 1.44 1.57 1.49 .43 70 310 1.56 .98 90 3710 5920 43 52 174 183 0 7134 266 6868 1.92 6316 6050 .521 1.735 .941 .795
11 1520 1468 189 232 1331 1236 1498 1523 196 247 1309 1291 0 0 386 527 67 131 100 96 100 95 2567 2600 1.077 .929 .986 .96 .9 .47 80 333 .98 .97 100 3860 5920 43 53 189 199 0 1769 280 1489 1.119 1835 1555 .894 1.188 .162 .249
12 2016 1735 188 212 1828 1523 2019 1594 196 235 1831 1382 0 0 527 779 69 141 100 99 100 94 3351 3213 1.2 .833 .755 .81 .74 .35 69 371 .88 .98 90 4010 5920 43 52 204 213 0 2090 255 1835 1.004 1921 1665 .996 .909 .006 -.137
13 3169 2302 190 214 2979 2088 3174 2321 194 237 2984 2107 0 0 526 737 63 144 100 100 100 97 5067 5091 1.427 .701 .706 .69 .71 .23 70 339 .75 .99 90 4150 5920 43 52 218 227 0 2774 258 2516 .844 2796 2539 1.184 .851 -.244 -.233
14 3359 8731 189 221 3170 8510 3353 8223 197 251 3164 8002 0 0 619 2480 68 157 100 100 100 100 11680 11166 .373 2.685 2.529 2.67 2.63 .48 70 344 2.6 .99 90 4320 5920 43 52 235 244 0 10520 266 10253 3.235 9908 9641 .309 3.047 1.694 1.607
15 1606 2625 183 220 1423 2405 1722 2668 192 242 1539 2448 0 0 453 917 66 141 100 100 100 97 3828 3987 .592 1.69 1.591 1.84 1.59 1.19 69 337 1.64 .99 90 4450 5920 43 52 248 257 0 3163 265 2898 2.036 3215 2950 .491 1.917 1.026 .938
16 7951 5701 187 207 7764 5494 7899 5603 195 227 7712 5396 0 0 987 1171 62 140 100 100 100 100 13258 13108 1.413 .708 .7 .7 .7 .12 70 351 .72 .99 90 4620 5920 43 52 265 274 0 6869 249 6620 .853 6751 6501 1.173 .843 -.23 -.246
17 2355 1985 196 216 2159 1769 2417 1910 199 229 2221 1694 0 0 480 796 62 132 100 98 100 96 3928 3915 1.22 .819 .763 .81 .79 .36 80 291 .86 .98 100 4760 5920 43 53 279 289 0 2392 260 2131 .987 2301 2041 1.013 .919 -.019 -.122
18 3516 3427 193 223 3323 3204 3747 3391 199 249 3554 3168 0 0 931 985 63 146 100 100 100 100 6527 6722 1.037 .964 .891 1.26 .94 1.57 80 279 .97 .99 100 4910 5930 44 54 294 304 0 4129 269 3860 1.162 4086 3817 .861 1.074 .216 .103
19 8070 6643 190 227 7880 6416 8100 6162 194 258 7910 5935 0 0 1900 1793 61 159 100 100 100 100 14296 13845 1.228 .814 .75 1 .79 1.25 86 288 .82 .98 100 5050 5920 43 53 308 318 0 8004 274 7730 .981 7424 7151 1.019 .904 -.028 -.146
20 1991 2445 184 219 1807 2226 2067 2374 192 243 1883 2155 0 0 485 725 67 182 100 100 99 100 4033 4038 .812 1.232 1.144 1.72 1.22 2.92 86 299 1.22 .97 100 5200 5930 44 54 323 333 0 2946 264 2682 1.484 2860 2596 .674 1.379 .57 .464

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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