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Sample GSM229018 Query DataSets for GSM229018
Status Public on Feb 24, 2012
Title shgc154|PR00036 Baboon
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 Baboon genomic DNA
Organism Papio hamadryas
Characteristics Baboon 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 1917 945 184 232 1733 713 1859 899 191 254 1675 667 0 0 494 384 65 154 100 95 100 90 2446 2342 2.431 .411 .398 .39 .43 .15 60 438 .51 .98 80 2310 6020 42 50 35 43 0 1188 292 896 .517 1130 838 1.934 .5 -.952 -.999
2 2635 1885 186 228 2449 1657 2558 1639 196 249 2372 1411 0 0 940 1131 73 139 100 100 100 100 4106 3783 1.478 .677 .595 .65 .65 .26 44 366 .72 .97 70 2460 6040 44 51 50 57 0 2369 287 2082 .85 2060 1773 1.176 .748 -.234 -.42
3 2904 1729 194 240 2710 1489 2538 1576 200 266 2344 1336 0 0 976 726 75 144 100 98 100 98 4199 3680 1.82 .549 .57 .53 .57 .18 52 378 .6 .99 80 2600 6030 43 51 64 72 0 2173 302 1871 .69 1981 1679 1.448 .716 -.534 -.481
4 2513 1382 196 271 2317 1111 2373 1170 202 290 2177 899 0 0 910 756 77 155 100 100 100 92 3428 3076 2.086 .479 .413 .46 .43 .21 52 381 .56 .97 80 2750 6030 43 51 79 87 0 1737 341 1396 .603 1470 1130 1.66 .519 -.731 -.946
5 1242 821 192 254 1050 567 1243 804 200 271 1051 550 0 0 185 288 72 162 100 94 100 79 1617 1601 1.852 .54 .523 .55 .51 .28 52 368 .68 .97 80 2880 6040 44 52 92 100 0 1032 319 713 .679 1010 691 1.474 .658 -.559 -.605
6 2653 1397 190 225 2463 1172 2446 1346 202 263 2256 1121 0 0 774 558 70 156 100 98 100 98 3635 3377 2.102 .476 .497 .46 .44 .18 44 405 .54 .99 70 3050 6030 43 50 109 116 0 1756 283 1473 .598 1691 1409 1.672 .624 -.742 -.679
7 1868 1521 191 246 1677 1275 1847 1499 201 284 1656 1253 0 0 582 494 70 160 100 100 100 99 2952 2909 1.315 .76 .757 .77 .78 .28 70 315 .84 .98 90 3190 6030 42 51 122 131 0 1911 309 1602 .955 1884 1575 1.047 .951 -.066 -.073
8 2081 1439 183 255 1898 1184 2081 1459 190 274 1898 1204 0 0 537 458 63 157 100 97 100 96 3082 3102 1.603 .624 .634 .66 .62 .36 69 311 .7 .98 90 3310 6030 42 51 134 143 0 1808 320 1488 .784 1833 1513 1.276 .797 -.351 -.327
9 1625 1721 187 254 1438 1467 1596 1704 195 269 1409 1450 0 0 304 512 66 157 100 100 100 100 2905 2859 .98 1.02 1.029 1.05 .98 .45 80 282 1.06 .98 100 3460 6040 43 53 149 159 0 2163 319 1844 1.282 2141 1822 .78 1.293 .358 .371
10 3263 3318 196 237 3067 3081 3146 3136 200 256 2950 2899 0 0 946 1168 68 144 100 100 100 100 6148 5849 .995 1.005 .983 1.03 .98 .35 80 279 1.02 .99 100 3600 6040 43 53 163 173 0 4170 298 3872 1.262 3941 3643 .792 1.235 .336 .304
11 1377 1292 184 241 1193 1051 1390 1266 192 259 1206 1025 0 0 248 438 67 146 100 100 100 99 2244 2231 1.135 .881 .85 .88 .91 .36 70 350 .95 .98 90 3750 6030 42 51 178 187 0 1624 303 1321 1.107 1591 1288 .903 1.068 .147 .095
12 1834 1470 181 242 1653 1228 1870 1425 187 262 1689 1183 0 0 563 576 61 146 100 99 97 99 2881 2872 1.346 .743 .7 .87 .75 1.04 69 367 .81 .98 90 3890 6040 43 52 192 201 0 1847 304 1543 .934 1791 1487 1.071 .88 -.099 -.184
13 2807 2457 182 261 2625 2196 2737 2457 190 274 2555 2196 0 0 484 625 66 152 100 100 100 100 4821 4751 1.195 .837 .859 .84 .84 .24 69 375 .9 .99 90 4040 6030 42 51 207 216 0 3088 328 2760 1.051 3088 2760 .951 1.08 .072 .111
14 3091 2760 190 252 2901 2508 3028 2611 197 270 2838 2359 0 0 654 836 66 151 100 100 100 100 5409 5197 1.157 .865 .831 .85 .85 .17 69 393 .91 .99 90 4200 6030 42 51 223 232 0 3468 317 3152 1.086 3281 2965 .92 1.045 .12 .063
15 1595 1249 188 242 1407 1007 1559 1239 193 270 1371 997 0 0 280 379 62 155 100 98 100 98 2414 2368 1.397 .716 .727 .75 .78 .3 52 347 .81 .98 80 4340 6040 44 52 238 246 0 1570 304 1265 .899 1557 1253 1.112 .914 -.153 -.13
16 6912 6035 187 243 6725 5792 6900 5972 191 269 6713 5729 0 0 1265 1395 61 155 100 100 100 100 12517 12442 1.161 .861 .853 .85 .85 .18 70 375 .89 .99 90 4510 6030 42 51 254 263 0 7584 305 7279 1.082 7505 7200 .924 1.072 .114 .101
17 2239 1800 195 254 2044 1546 2174 1717 195 274 1979 1463 0 0 496 570 65 150 100 100 100 100 3590 3442 1.322 .756 .739 .77 .71 .29 70 315 .82 .98 90 4650 6030 42 51 268 277 0 2262 319 1943 .951 2158 1839 1.052 .929 -.073 -.106
18 3316 3234 185 258 3131 2976 3472 3165 194 271 3287 2907 0 0 642 962 63 154 100 100 100 100 6107 6194 1.052 .95 .884 .94 .93 .26 80 289 .98 .99 100 4800 6040 43 53 283 293 0 4064 324 3740 1.194 3977 3653 .837 1.111 .256 .152
19 7832 7526 185 242 7647 7284 7516 6770 196 262 7331 6528 0 0 1951 2631 67 151 100 100 100 100 14931 13859 1.05 .953 .89 1.04 .9 .81 86 284 .96 .98 100 4930 6040 43 53 296 306 0 9458 304 9154 1.197 8508 8204 .835 1.119 .259 .162
20 2036 1830 186 238 1850 1592 2010 1697 190 261 1824 1459 0 0 379 609 59 150 100 100 100 99 3442 3283 1.162 .861 .8 .86 .82 .34 80 285 .92 .98 100 5090 6050 44 54 312 322 0 2300 299 2001 1.081 2133 1833 .925 1.005 .113 .007

Total number of rows: 41472

Table truncated, full table size 9450 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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