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Sample GSM90761 Query DataSets for GSM90761
Status Public on Jan 06, 2006
Title HUMAN 3 [HSJ (human male) vs. HSJ (human 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 Human male genomic DNA
Organism Homo sapiens
Characteristics Human male genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Comparative genomics, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37979.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) [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 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
1 624 677 140 175 484 502 658 668 149 176 518 493 0 0 207 220 45 46 100 100 100 100 986 1011 .964 1.037 .952 1.021 1.082 1.632 32 171 1.07 .86 60 1830 7610 50 56 64 70 0 767 198 569 1.175 757 559 .851 1.079 .233 .109
2 1267 1363 150 168 1117 1195 1298 1417 154 174 1148 1249 0 0 372 393 46 55 100 100 100 100 2312 2397 .935 1.07 1.088 1.07 1.046 1.242 32 183 1.035 .95 70 1970 7610 49 56 77 84 0 1545 190 1354 1.212 1606 1415 .825 1.233 .278 .302
3 244 292 148 182 96 110 154 200 152 185 6 18 0 0 250 270 47 53 30 31 20 16 206 24 .873 1.146 3 1.176 1.14 3.079 80 393 1.115 .88 100 2100 7600 47 57 89 99 -50 331 206 125 1.299 227 20 .77 3.4 .377 1.765
4 706 784 149 180 557 604 627 673 150 180 478 493 0 0 386 345 42 49 100 100 100 90 1161 971 .922 1.084 1.031 1.112 1.192 1.863 32 205 1.01 .91 70 2270 7610 49 56 107 114 0 888 204 684 1.229 763 559 .814 1.169 .297 .225
5 1666 1743 145 190 1521 1553 1592 1664 160 207 1447 1474 0 0 634 656 91 162 100 98 100 98 3074 2921 .979 1.021 1.019 .968 1.023 2.027 52 241 1.021 .95 80 2410 7610 49 57 121 129 0 1975 215 1760 1.157 1886 1670 .864 1.154 .211 .207
6 1510 1660 147 208 1363 1452 1404 1662 166 246 1257 1454 0 0 1037 1024 114 214 93 87 84 78 2815 2711 .939 1.065 1.157 1.195 1.096 1.909 32 141 1.021 .94 60 2530 7590 48 54 134 140 0 1881 236 1646 1.207 1883 1648 .828 1.311 .272 .391
7 1108 1201 144 191 964 1010 1129 1320 148 196 985 1129 0 0 510 496 46 54 100 96 96 96 1974 2114 .954 1.048 1.146 1.043 1.085 1.434 32 157 1.027 .95 60 2710 7610 50 56 152 158 0 1361 216 1145 1.187 1496 1279 .842 1.299 .248 .377
8 1856 1767 152 201 1704 1566 1838 1700 224 262 1686 1499 0 0 586 423 228 191 100 100 100 100 3270 3185 1.088 .919 .889 .954 .847 1.282 12 87 .904 .95 50 2820 7590 48 53 163 168 0 2002 228 1775 1.041 1927 1699 .96 1.008 .059 .011
9 1344 1243 148 198 1196 1045 1329 1250 176 227 1181 1052 0 0 352 280 256 253 100 98 97 95 2241 2233 1.144 .874 .891 .875 .882 1.309 80 394 .853 .96 110 2980 7610 47 58 176 187 0 1409 224 1184 .99 1417 1192 1.01 1.009 -.014 .014
10 488 512 143 186 345 326 484 519 155 199 341 333 0 0 144 126 68 81 96 98 88 86 671 674 1.058 .945 .977 .977 .908 1.884 80 264 .927 .83 100 3120 7610 48 58 191 201 0 580 211 369 1.071 588 377 .934 1.107 .099 .146
11 1280 1163 142 191 1138 972 1286 1153 155 200 1144 962 0 0 386 259 68 66 100 100 100 100 2110 2106 1.171 .854 .841 .884 .859 1.36 80 339 .818 .95 110 3260 7600 46 57 204 215 0 1318 216 1102 .968 1307 1090 1.033 .953 -.047 -.069
12 956 906 141 197 815 709 950 899 152 202 809 702 0 0 221 184 66 61 100 100 100 100 1524 1511 1.15 .87 .868 .872 .867 1.242 80 348 .875 .94 110 3410 7600 46 57 219 230 0 1027 223 803 .986 1019 796 1.014 .983 -.021 -.024
13 1943 1934 140 185 1803 1749 1948 1943 145 189 1808 1758 0 0 597 517 45 50 100 100 100 100 3552 3566 1.031 .97 .972 .981 .967 1.226 80 354 .946 .97 110 3550 7600 46 57 233 244 0 2192 210 1982 1.099 2202 1992 .91 1.102 .137 .14
14 1746 1618 146 185 1600 1433 1712 1560 149 192 1566 1375 0 0 489 381 51 54 100 100 100 100 3033 2941 1.117 .896 .878 .913 .897 1.266 80 380 .881 .96 110 3700 7600 46 57 248 259 0 1834 210 1624 1.015 1768 1558 .985 .995 .021 -.007
15 861 817 144 194 717 623 836 814 151 203 692 620 0 0 186 127 67 70 100 100 100 100 1340 1312 1.151 .869 .896 .878 .861 1.327 80 372 .875 .92 110 3850 7600 46 57 263 274 0 926 220 706 .985 922 703 1.016 1.015 -.022 .022
16 436 499 154 200 282 299 169 209 274 302 15 9 0 0 1173 1197 556 478 8 12 5 7 581 24 .943 1.06 .6 1.187 1.083 2.85 80 339 .985 .96 100 4000 7600 47 57 279 289 -50 566 227 339 1.202 237 10 .832 .68 .265 -.556
17 2248 1994 160 203 2088 1791 2265 2050 469 463 2105 1847 0 0 703 506 1035 903 93 93 52 53 3879 3952 1.166 .858 .877 .873 .839 1.259 80 355 .892 .97 110 4150 7600 46 57 293 304 0 2260 230 2030 .972 2323 2093 1.029 .994 -.041 -.008
18 195 234 140 185 55 49 155 195 160 203 15 10 0 0 144 147 108 120 17 12 8 7 104 25 1.122 .891 .667 1.065 1.103 4.53 80 278 1.004 .63 100 4290 7600 47 57 308 318 -50 265 210 56 1.01 221 11 .99 .756 .014 -.404
19 5320 4599 137 185 5183 4414 5314 4704 147 188 5177 4519 0 0 1798 1219 61 54 100 100 100 100 9597 9696 1.174 .852 .873 .876 .849 1.19 80 295 .827 .98 100 4430 7600 47 57 322 332 0 5212 210 5002 .965 5331 5121 1.036 .989 -.051 -.016
20 1050 965 137 177 913 788 1047 979 144 179 910 802 0 0 292 172 50 51 100 100 100 100 1701 1712 1.159 .863 .881 .892 .861 1.367 80 318 .833 .94 100 4580 7600 47 57 337 347 0 1094 201 893 .978 1109 909 1.022 .999 -.032 -.002

Total number of rows: 43104

Table truncated, full table size 9960 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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