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Sample GSM90759 Query DataSets for GSM90759
Status Public on Jan 06, 2006
Title CHIMP 4 [HSJ (human male) vs. PTS (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/2003-02/37978.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
1 595 535 140 149 455 386 602 544 141 161 462 395 0 0 194 160 44 54 100 96 100 93 841 857 1.179 .848 .855 .868 .813 1.579 32 165 .77 .88 60 1810 7600 49 55 62 68 0 636 177 459 1.009 647 470 .991 1.017 .013 .024
2 1001 904 125 148 876 756 963 885 131 156 838 737 0 0 375 346 41 56 100 100 100 100 1632 1575 1.159 .863 .879 .844 .864 1.547 32 177 .869 .92 70 1970 7600 48 55 77 84 0 1075 176 899 1.026 1053 876 .974 1.046 .038 .065
3 140 170 127 150 13 20 131 161 132 155 4 11 0 0 80 95 42 54 21 16 5 6 33 15 .65 1.538 2.75 .842 .85 3.685 80 407 .558 .73 100 2080 7600 47 57 87 97 -50 202 178 24 1.83 191 13 .547 3.27 .872 1.71
4 783 725 131 154 652 571 783 667 138 165 652 513 0 0 306 220 51 71 100 100 100 100 1223 1165 1.142 .876 .787 .942 .738 1.635 12 104 .813 .84 50 2270 7600 49 54 108 113 0 862 183 679 1.042 793 610 .96 .936 .059 -.096
5 1675 1503 125 150 1550 1353 1756 1458 134 171 1631 1308 0 0 711 641 57 79 100 100 100 100 2903 2939 1.146 .873 .802 .869 .883 1.454 32 165 .862 .93 60 2400 7610 50 56 121 127 0 1787 178 1609 1.038 1734 1556 .963 .954 .054 -.068
6 1973 1972 152 173 1821 1799 2554 2266 248 274 2402 2093 0 0 1017 1064 345 307 100 100 83 83 3620 4495 1.012 .988 .871 .99 .924 1.253 12 88 .975 .97 50 2510 7580 47 52 132 137 0 2345 206 2139 1.175 2695 2489 .851 1.036 .233 .051
7 342 370 138 157 204 213 156 176 159 180 18 19 0 0 480 481 166 151 17 16 15 15 417 37 .958 1.044 1.056 1.16 1.064 3.075 80 427 .973 .93 100 2670 7600 47 57 146 156 -50 440 187 253 1.242 209 23 .805 1.255 .312 .328
8 1818 1719 143 166 1675 1553 1933 1624 161 171 1790 1458 0 0 580 520 121 84 100 100 100 100 3228 3248 1.079 .927 .815 .912 .903 1.405 12 93 .896 .95 50 2800 7590 48 53 161 166 0 2044 197 1847 1.103 1931 1734 .907 .969 .141 -.046
9 1148 1025 132 161 1016 864 1166 1105 142 167 1034 944 0 0 357 316 70 63 98 97 98 95 1880 1978 1.176 .85 .913 .8 .83 1.514 80 395 .845 .96 100 2960 7600 47 57 175 185 0 1219 191 1028 1.011 1314 1123 .989 1.086 .016 .119
10 306 272 134 157 172 115 183 181 139 166 49 24 0 0 246 177 48 56 50 48 41 38 287 73 1.496 .669 .49 .639 .738 3.161 80 331 .692 .76 100 3110 7600 47 57 190 200 -50 323 187 137 .795 215 29 1.258 .583 -.331 -.78
11 1092 877 138 166 954 711 1057 875 149 179 919 709 0 0 277 242 73 77 100 100 100 100 1665 1628 1.342 .745 .771 .721 .753 1.386 52 281 .77 .93 90 3250 7590 46 55 204 213 0 1043 197 846 .886 1041 843 1.128 .918 -.174 -.124
12 934 757 138 163 796 594 911 784 146 170 773 621 0 0 257 201 67 70 100 100 100 98 1390 1394 1.34 .746 .803 .739 .718 1.362 80 366 .743 .94 100 3400 7600 47 57 219 229 0 900 194 706 .887 932 739 1.127 .955 -.172 -.066
13 1778 1603 139 155 1639 1448 1808 1689 158 174 1669 1534 0 0 471 502 232 163 100 98 96 95 3087 3203 1.132 .883 .919 .86 .89 1.384 80 326 .903 .96 100 3550 7600 47 57 234 244 0 1906 184 1722 1.051 2009 1824 .952 1.093 .071 .128
14 1404 1242 142 152 1262 1090 1417 1256 145 167 1275 1104 0 0 343 312 45 59 100 100 100 100 2352 2379 1.158 .864 .866 .864 .842 1.319 80 334 .856 .95 100 3690 7600 47 57 248 258 0 1477 181 1296 1.027 1494 1313 .974 1.03 .039 .042
15 929 751 140 160 789 591 935 748 143 171 795 588 0 0 172 143 44 63 100 100 100 100 1380 1383 1.335 .749 .74 .744 .709 1.273 80 315 .749 .92 100 3840 7600 47 57 263 273 0 893 190 703 .891 890 699 1.123 .88 -.167 -.185
16 363 337 137 153 226 184 147 142 143 161 10 -11 0 0 805 656 48 55 30 25 17 20 410 -1 1.228 .814 null 1.044 1.018 3.537 80 342 .81 .95 100 3980 7600 47 57 277 287 -50 401 182 219 .968 169 -13 1.033 null -.047 null
17 2103 1693 135 161 1968 1532 2192 1795 142 166 2057 1634 0 0 627 532 47 54 100 100 100 100 3500 3691 1.285 .778 .794 .76 .763 1.421 80 337 .777 .96 100 4130 7600 47 57 292 302 0 2013 191 1822 .926 2135 1943 1.08 .945 -.111 -.082
18 151 173 140 162 11 11 142 165 147 167 2 3 0 0 65 67 47 57 18 18 8 6 22 5 1 1 1.5 1.152 1.13 3.31 80 316 1.07 .33 100 4280 7600 47 57 307 317 -50 206 193 13 1.189 196 4 .841 1.784 .25 .835
19 6830 5657 140 165 6690 5492 7188 5976 147 172 7048 5811 0 0 2063 1757 49 63 100 100 100 100 12182 12859 1.218 .821 .824 .802 .83 1.321 80 304 .819 .98 100 4430 7600 47 57 322 332 0 6728 196 6531 .976 7107 6911 1.024 .981 -.035 -.028
20 1546 1231 135 165 1411 1066 1617 1243 139 171 1482 1078 0 0 461 360 47 60 98 98 98 98 2477 2560 1.324 .755 .727 .783 .725 1.628 80 303 .752 .95 100 4580 7600 47 57 337 347 0 1464 196 1268 .898 1478 1282 1.113 .865 -.154 -.209

Total number of rows: 43104

Table truncated, full table size 10000 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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