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Sample GSM229020 Query DataSets for GSM229020
Status Public on Feb 24, 2012
Title shgc147|PR00644 Marmoset
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 Marmoset genomic DNA
Organism Callithrix sp.
Characteristics Marmoset 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 1138 611 122 154 1016 457 1132 566 127 187 1010 412 0 0 244 423 50 142 100 76 100 66 1473 1422 2.223 .45 .408 .46 .41 .32 70 401 .57 .94 90 2470 6020 53 62 50 59 0 690 174 516 .508 639 465 1.968 .461 -.977 -1.118
2 1298 815 120 134 1178 681 1311 718 129 181 1191 584 0 0 573 433 49 157 100 93 100 78 1859 1775 1.73 .578 .49 .75 .53 .82 69 337 .62 .96 90 2620 6030 54 63 65 74 0 921 151 769 .653 811 660 1.531 .554 -.615 -.852
3 1638 1017 120 134 1518 883 1615 943 127 170 1495 809 0 0 425 512 52 144 100 97 100 88 2401 2304 1.719 .582 .541 .57 .52 .33 60 363 .63 .97 80 2760 6020 54 62 80 88 0 1149 151 997 .657 1065 914 1.522 .611 -.606 -.71
4 1385 1013 115 160 1270 853 1318 982 121 189 1203 822 0 0 460 560 47 151 100 90 100 82 2123 2025 1.489 .672 .683 .68 .63 .34 60 375 .75 .97 80 2910 6020 54 62 95 103 0 1144 181 963 .759 1109 928 1.318 .772 -.398 -.374
5 855 1074 118 159 737 915 888 1107 121 199 770 948 0 0 276 387 45 158 97 97 97 95 1652 1718 .805 1.242 1.231 1.44 1.27 1.24 60 362 1.22 .96 80 3040 6030 55 63 108 116 0 1213 180 1034 1.402 1250 1071 .713 1.391 .488 .476
6 1417 800 123 146 1294 654 1380 694 127 192 1257 548 0 0 473 527 50 156 100 84 100 71 1948 1805 1.979 .505 .436 .54 .48 .49 51 415 .58 .96 80 3200 6030 55 63 124 132 0 904 165 739 .571 784 619 1.752 .492 -.809 -1.022
7 1244 1182 120 141 1124 1041 1281 1103 122 183 1161 962 0 0 292 518 44 144 100 99 100 94 2165 2123 1.08 .926 .829 .96 .85 .53 70 311 .95 .97 90 3350 6030 54 63 138 147 0 1335 159 1176 1.046 1246 1087 .956 .936 .065 -.096
8 1370 1493 117 150 1253 1343 1412 1455 120 184 1295 1305 0 0 471 625 47 146 99 99 99 99 2596 2600 .933 1.072 1.008 1.13 1.08 .53 69 300 1.09 .97 90 3470 6030 54 63 150 159 0 1686 169 1517 1.211 1643 1474 .826 1.138 .276 .187
9 1085 931 120 147 965 784 1109 908 123 183 989 761 0 0 205 381 46 144 100 95 100 93 1749 1750 1.231 .812 .769 .82 .87 .4 80 304 .88 .97 100 3620 6030 54 64 165 175 0 1052 166 886 .918 1026 860 1.09 .869 -.124 -.202
10 2335 1912 118 134 2217 1778 2247 1937 124 176 2129 1803 0 0 545 681 49 144 100 99 100 99 3995 3932 1.247 .802 .847 .81 .79 .32 80 290 .84 .98 100 3770 6030 54 64 180 190 0 2160 151 2008 .906 2188 2037 1.104 .957 -.143 -.064
11 965 769 121 149 844 620 975 736 125 180 854 587 0 0 168 362 50 138 100 96 100 80 1464 1441 1.361 .735 .687 .77 .72 .44 70 335 .82 .97 90 3910 6030 54 63 194 203 0 869 168 700 .83 831 663 1.205 .776 -.269 -.365
12 1208 715 119 161 1089 554 1182 685 125 186 1063 524 0 0 344 340 72 141 100 87 100 78 1643 1587 1.966 .509 .493 .5 .5 .28 69 361 .61 .97 90 4060 6030 54 63 209 218 0 808 182 626 .575 774 592 1.74 .557 -.799 -.845
13 1825 1564 122 160 1703 1404 1883 1590 131 197 1761 1430 0 0 417 655 74 159 100 98 100 95 3107 3191 1.213 .824 .812 .88 .76 .64 80 316 .86 .97 100 4210 6030 54 64 224 234 0 1767 181 1586 .931 1796 1615 1.074 .917 -.103 -.125
14 1837 1929 124 151 1713 1778 1840 1857 128 184 1716 1706 0 0 358 714 46 141 100 99 100 98 3491 3422 .963 1.038 .994 1.04 1.03 .39 80 326 1.06 .98 100 4370 6030 54 64 240 250 0 2179 171 2008 1.172 2098 1927 .853 1.123 .229 .167
15 918 808 119 140 799 668 974 729 121 171 855 589 0 0 265 456 43 132 100 88 97 86 1467 1444 1.196 .836 .689 1.39 .87 2.57 64 294 .88 .94 90 4510 6030 54 63 254 263 0 913 158 755 .944 823 665 1.059 .778 -.083 -.362
16 6586 10459 120 148 6466 10311 5998 8259 130 179 5878 8111 0 0 2935 5873 56 142 100 100 100 100 16777 13989 .627 1.595 1.38 1.65 1.54 .76 97 320 1.6 .97 110 4660 6030 53 64 268 279 0 11814 167 11647 1.801 9329 9162 .555 1.559 .849 .64
17 1683 1588 124 160 1559 1428 1683 1623 135 197 1559 1463 0 0 358 629 61 164 100 96 100 95 2987 3022 1.092 .916 .938 1 .91 .68 80 276 .96 .97 100 4810 6030 54 64 284 294 0 1794 181 1613 1.035 1833 1653 .967 1.06 .049 .084
18 2531 2399 125 162 2406 2237 2549 2353 137 197 2424 2191 0 0 320 840 60 157 100 99 100 97 4643 4615 1.076 .93 .904 .94 .94 .34 70 299 .97 .98 90 4950 6030 54 63 298 307 0 2710 183 2527 1.05 2658 2475 .952 1.021 .071 .03
19 4815 4022 130 146 4685 3876 5196 4109 139 182 5066 3963 0 0 1587 1143 57 153 99 100 98 100 8561 9029 1.209 .827 .782 2.17 .78 6.05 97 290 .82 .97 110 5090 6030 53 64 311 322 0 4543 165 4378 .934 4641 4476 1.07 .884 -.098 -.179
20 1400 1155 124 151 1276 1004 1392 1171 127 190 1268 1020 0 0 224 490 45 153 100 96 100 90 2280 2288 1.271 .787 .804 .81 .75 .38 80 293 .85 .97 100 5250 6040 55 65 328 338 0 1305 171 1134 .889 1323 1152 1.125 .909 -.17 -.138

Total number of rows: 41472

Table truncated, full table size 9329 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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