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Sample GSM90758 Query DataSets for GSM90758
Status Public on Jan 06, 2006
Title CHIMP 1 [HSJ (human male) vs. PTC (Chimp male)]
Sample type genomic
 
Channel 1
Source name Human male genomic DNA
Organism Homo sapiens
Characteristics Human male genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Chimpanzee male genomic DNA
Organism Homo sapiens
Characteristics Chimpanzee male genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37976.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 Jan 05, 2006
Last update date Feb 23, 2012
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 GPL1448
Series (2)
GSE3980 Lineage-specific gene duplication and loss in human and great ape evolution
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
1 588 668 147 167 441 501 569 719 148 176 422 552 0 0 236 233 45 61 100 100 100 93 942 974 .88 1.136 1.308 1.157 1.051 1.645 32 158 1.092 .87 60 1860 7720 61 67 67 73 0 748 187 561 1.273 805 618 .786 1.465 .348 .551
2 1046 1128 135 163 911 965 1073 1159 138 170 938 996 0 0 421 419 47 56 100 100 100 98 1876 1934 .944 1.059 1.062 1.074 1.033 1.351 52 221 1.042 .95 80 2000 7720 60 68 80 88 0 1264 183 1081 1.187 1298 1116 .843 1.189 .247 .25
3 266 256 140 166 126 90 159 193 142 174 19 27 0 0 270 170 46 61 33 38 25 23 216 46 1.4 .714 1.421 .942 .839 2.724 80 371 .657 .75 100 2130 7710 58 68 92 102 -50 287 186 101 .8 216 30 1.25 1.592 -.322 .671
4 595 673 137 171 458 502 511 597 146 181 374 426 0 0 312 301 53 56 96 96 87 93 960 800 .912 1.096 1.139 1.113 1.098 1.788 32 165 1.017 .91 60 2300 7720 61 67 111 117 0 754 192 562 1.228 669 477 .814 1.276 .296 .352
5 1761 1643 143 167 1618 1476 1797 1649 146 185 1654 1482 0 0 615 524 49 75 100 100 100 100 3094 3136 1.096 .912 .896 .932 .935 1.301 32 203 .881 .96 70 2440 7720 60 67 124 131 0 1840 187 1653 1.022 1847 1660 .979 1.004 .031 .005
6 1491 1703 145 167 1346 1536 1235 1335 151 193 1090 1168 0 0 907 1067 65 102 96 93 96 90 2882 2258 .876 1.141 1.072 1.083 1.009 1.297 32 157 1.162 .95 60 2570 7700 59 65 138 144 0 1908 187 1721 1.278 1495 1308 .782 1.2 .354 .263
7 1415 1505 140 180 1275 1325 1419 1553 143 184 1279 1373 0 0 295 352 65 55 100 100 100 100 2600 2652 .962 1.039 1.073 1.023 1.038 1.348 12 104 1.062 .93 50 2740 7710 60 65 155 160 0 1686 202 1484 1.164 1740 1538 .859 1.202 .219 .266
8 1350 1273 142 167 1208 1106 1241 1301 157 184 1099 1134 0 0 548 517 65 82 100 100 100 100 2314 2233 1.092 .916 1.032 .906 .914 1.427 32 131 .907 .93 60 2870 7700 59 65 168 174 0 1426 187 1239 1.026 1457 1270 .975 1.156 .036 .209
9 1204 1165 137 179 1067 986 1194 1202 144 188 1057 1023 0 0 333 311 46 64 100 100 100 98 2053 2080 1.082 .924 .968 .916 .91 1.251 80 359 .932 .96 100 2990 7710 58 68 178 188 0 1305 201 1104 1.035 1346 1146 .966 1.084 .05 .117
10 445 422 138 182 307 240 448 414 145 189 310 232 0 0 129 108 44 69 98 100 96 78 547 542 1.279 .782 .748 .78 .781 1.666 52 276 .824 .75 90 3150 7710 58 67 194 203 0 473 204 269 .876 464 260 1.142 .838 -.192 -.254
11 1165 1085 139 179 1026 906 1220 1112 146 189 1081 933 0 0 315 259 48 69 100 100 100 100 1932 2014 1.132 .883 .863 .894 .864 1.334 80 330 .884 .94 100 3290 7710 58 68 208 218 0 1215 201 1015 .989 1246 1045 1.011 .967 -.016 -.049
12 794 819 133 175 661 644 773 804 141 184 640 629 0 0 217 208 47 65 100 98 100 98 1305 1269 1.026 .974 .983 .962 1.029 1.439 80 311 .98 .9 100 3440 7710 58 68 223 233 0 917 196 721 1.091 901 705 .916 1.101 .126 .139
13 1538 1618 135 172 1403 1446 1511 1646 140 185 1376 1474 0 0 395 405 50 73 100 100 100 100 2849 2850 .97 1.031 1.071 1.03 1.009 1.227 80 311 1.019 .96 100 3580 7710 58 68 237 247 0 1812 193 1620 1.154 1844 1651 .866 1.2 .207 .263
14 1370 1348 135 162 1235 1186 1360 1287 140 176 1225 1125 0 0 410 373 50 69 100 100 100 100 2421 2350 1.041 .96 .918 .965 .955 1.234 80 336 .971 .96 100 3740 7710 58 68 253 263 0 1510 181 1329 1.076 1442 1260 .93 1.029 .105 .041
15 814 782 131 163 683 619 800 760 137 174 669 597 0 0 187 166 43 57 100 100 100 100 1302 1266 1.103 .906 .892 .907 .91 1.333 80 296 .88 .92 100 3880 7710 58 68 267 277 0 876 183 693 1.015 851 669 .985 1 .022 -.001
16 317 318 131 170 186 148 154 174 136 179 23 4 0 0 818 552 45 68 31 18 16 11 334 27 1.257 .796 .174 1.31 1.353 3.832 80 329 .646 .82 100 4030 7700 57 67 282 292 -50 356 190 166 .891 195 4 1.122 .195 -.166 -2.36
17 2132 1997 129 158 2003 1839 2189 2011 136 171 2060 1853 0 0 589 498 47 69 100 100 100 100 3842 3913 1.089 .918 .9 .922 .909 1.212 80 308 .912 .97 100 4170 7710 58 68 296 306 0 2237 177 2060 1.028 2253 2076 .972 1.008 .04 .011
18 168 209 135 165 33 44 144 179 140 176 9 14 0 0 90 109 46 61 30 28 12 13 77 23 .75 1.333 1.556 1.1 1.106 2.905 80 327 1.926 .45 100 4320 7700 57 67 311 321 -50 234 185 49 1.494 201 16 .67 1.742 .579 .801
19 6840 5981 138 175 6702 5806 7223 6272 142 180 7085 6097 0 0 2320 1904 44 58 100 100 100 100 12508 13182 1.154 .866 .861 .873 .868 1.178 80 339 .858 .99 110 4470 7710 57 68 325 336 0 6700 196 6504 .97 7026 6830 1.031 .964 -.043 -.053
20 1367 1157 134 162 1233 995 1399 1151 138 170 1265 989 0 0 400 352 42 54 100 98 100 98 2228 2254 1.239 .807 .782 .802 .843 1.296 80 313 .809 .94 100 4610 7710 58 68 340 350 0 1296 181 1115 .904 1289 1108 1.106 .876 -.146 -.191

Total number of rows: 43104

Table truncated, full table size 9980 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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