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Sample GSM90769 Query DataSets for GSM90769
Status Public on Jan 06, 2006
Title HUMAN 5 [HSJ (human male) vs. HSE (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/2003-02/37980.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
1 799 830 156 187 643 643 724 802 172 200 568 615 0 0 302 295 100 87 98 98 92 96 1286 1183 1 1 1.083 .995 1.068 1.721 52 270 .989 .9 80 1900 7670 55 63 70 78 0 892 201 691 1.074 862 661 .931 1.163 .104 .218
2 1842 1791 160 195 1682 1596 1770 1754 196 224 1610 1559 0 0 605 501 158 143 100 100 100 100 3278 3169 1.054 .949 .968 .971 .991 1.299 32 213 .925 .95 70 2040 7650 53 60 84 91 0 1924 210 1715 1.019 1885 1675 .981 1.04 .028 .057
3 734 742 155 198 579 544 711 713 159 203 556 515 0 0 413 335 51 55 90 96 84 87 1123 1071 1.064 .94 .926 1.054 .981 1.66 32 164 .877 .93 60 2200 7670 56 62 101 107 0 797 213 584 1.009 766 553 .991 .995 .014 -.007
4 914 1004 161 187 753 817 966 902 164 189 805 715 0 0 387 362 46 55 100 100 100 100 1570 1520 .922 1.085 .888 1.179 1.099 1.519 32 188 1.001 .92 70 2350 7670 55 62 115 122 0 1079 201 878 1.166 969 768 .858 .954 .221 -.067
5 2510 2512 165 198 2345 2314 2455 2358 173 208 2290 2160 0 0 1200 1290 57 60 100 100 98 100 4659 4450 1.013 .987 .943 .986 .998 1.455 52 236 1.009 .97 80 2480 7670 55 63 128 136 0 2699 213 2486 1.06 2533 2321 .943 1.013 .084 .019
6 2786 3030 160 192 2626 2838 2843 2993 166 200 2683 2801 0 0 1411 1419 52 58 100 100 100 100 5464 5484 .925 1.081 1.044 1.114 1.123 1.38 52 315 1.048 .94 90 2620 7660 53 62 141 150 0 3255 206 3049 1.161 3216 3009 .861 1.122 .216 .166
7 1922 1895 155 186 1767 1709 1973 1937 158 191 1818 1751 0 0 528 466 48 58 100 100 100 100 3476 3569 1.034 .967 .963 .983 .951 1.252 32 192 .957 .96 70 2770 7670 55 62 157 164 0 2036 200 1836 1.039 2081 1881 .962 1.035 .055 .049
8 1567 1613 166 193 1401 1420 1364 1612 198 227 1198 1419 0 0 661 614 197 175 96 96 93 93 2821 2617 .987 1.014 1.184 1.032 1.112 1.44 32 212 .977 .96 70 2900 7650 53 60 170 177 0 1733 207 1526 1.089 1732 1525 .918 1.273 .123 .348
9 1713 1567 153 187 1560 1380 1708 1540 175 205 1555 1353 0 0 401 343 147 135 100 100 100 100 2940 2908 1.13 .885 .87 .888 .871 1.258 80 376 .881 .96 100 3060 7660 53 63 185 195 0 1684 201 1483 .95 1655 1454 1.052 .935 -.073 -.097
10 527 498 157 183 370 315 536 501 164 193 379 318 0 0 146 137 57 62 98 97 96 92 685 697 1.175 .851 .839 .805 .876 1.889 80 345 .833 .81 110 3210 7660 52 63 199 210 0 535 197 338 .915 538 342 1.093 .901 -.129 -.15
11 1387 1361 161 206 1226 1155 1401 1302 164 211 1240 1096 0 0 333 312 49 57 100 100 100 100 2381 2336 1.061 .942 .884 .947 .924 1.248 80 358 .911 .94 110 3350 7650 51 62 213 224 0 1462 221 1241 1.012 1399 1178 .988 .95 .017 -.075
12 1055 1009 158 201 897 808 1021 973 162 206 863 772 0 0 292 265 46 55 100 100 100 100 1705 1635 1.11 .901 .895 .898 .903 1.334 80 314 .894 .94 100 3500 7660 53 63 229 239 0 1084 216 868 .968 1045 829 1.033 .961 -.047 -.057
13 2061 2093 155 195 1906 1898 2041 2101 162 201 1886 1906 0 0 646 641 49 54 100 100 100 100 3804 3792 1.004 .996 1.011 .998 .986 1.235 80 369 1 .97 110 3640 7650 51 62 242 253 0 2249 210 2039 1.07 2257 2048 .935 1.086 .097 .119
14 1783 1607 155 199 1628 1408 1741 1553 163 206 1586 1354 0 0 529 444 53 60 100 100 100 100 3036 2940 1.156 .865 .854 .869 .858 1.203 80 328 .859 .97 100 3790 7650 52 62 258 268 0 1727 214 1513 .929 1669 1455 1.076 .917 -.106 -.125
15 1016 888 153 195 863 693 1025 902 160 206 872 707 0 0 194 167 63 68 100 100 100 100 1556 1579 1.245 .803 .811 .799 .787 1.306 80 337 .808 .93 110 3930 7660 52 63 271 282 0 954 210 745 .863 969 760 1.159 .871 -.213 -.199
16 438 546 155 198 283 348 185 216 163 207 30 18 0 0 970 1114 63 61 25 35 15 25 631 48 .813 1.23 .6 1.043 1.125 3.711 80 345 1.123 .88 100 4080 7650 52 62 287 297 -50 587 213 374 1.321 232 19 .757 .645 .402 -.633
17 2671 2328 155 201 2516 2127 2832 2400 164 203 2677 2199 0 0 803 585 54 54 100 100 100 100 4643 4876 1.183 .845 .821 .862 .855 1.274 80 320 .828 .97 100 4230 7650 52 62 302 312 0 2501 216 2285 .908 2579 2363 1.101 .883 -.139 -.18
18 216 253 158 198 58 55 170 204 162 201 12 6 0 0 189 207 50 54 28 25 11 11 113 18 1.055 .948 .5 1.259 1.432 5.02 80 301 1.16 .73 100 4370 7650 52 62 316 326 -50 272 213 59 1.019 219 6 .982 .537 .027 -.896
19 6918 6402 156 216 6762 6186 7180 6691 161 217 7024 6475 0 0 2416 1789 84 72 100 100 100 100 12948 13499 1.093 .915 .922 .939 .94 1.19 80 297 .884 .98 100 4520 7650 52 62 331 341 0 6878 232 6646 .983 7189 6957 1.017 .99 -.025 -.014
20 1478 1321 149 209 1329 1112 1551 1356 157 212 1402 1147 0 0 353 328 84 73 100 100 100 100 2441 2549 1.195 .837 .818 .828 .838 1.349 80 304 .855 .94 100 4660 7650 52 62 345 355 0 1419 225 1195 .899 1457 1232 1.112 .879 -.154 -.186

Total number of rows: 43104

Table truncated, full table size 10018 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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