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Sample GSM229017 Query DataSets for GSM229017
Status Public on Feb 24, 2012
Title shgc153|PR00721 Gibbon
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 Gibbon genomic DNA
Organism Hylobates sp.
Characteristics Gibbon 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 2486 1360 212 257 2274 1103 2384 1321 219 274 2172 1064 0 0 739 545 78 147 100 97 100 95 3377 3236 2.062 .485 .49 .5 .47 .23 64 403 .56 .98 90 2320 6310 42 51 35 44 0 1843 348 1494 .657 1790 1442 1.522 .664 -.606 -.591
2 3695 2039 216 260 3479 1779 3554 1934 224 285 3338 1674 0 0 881 793 78 151 100 100 100 100 5258 5012 1.956 .511 .501 .49 .49 .14 44 367 .56 .99 70 2470 6320 44 51 51 58 0 2763 352 2410 .693 2620 2268 1.443 .679 -.529 -.558
3 3467 2805 218 271 3249 2534 3322 2483 222 294 3104 2212 0 0 1260 1420 79 162 100 100 100 100 5783 5316 1.282 .78 .713 .76 .76 .2 60 382 .82 .99 80 2610 6310 43 51 65 73 0 3800 367 3433 1.057 3364 2997 .946 .966 .08 -.051
4 3101 2070 209 264 2892 1806 3040 1915 219 281 2831 1651 0 0 1074 1065 81 148 100 100 100 98 4698 4482 1.601 .624 .583 .59 .58 .22 52 343 .67 .98 80 2760 6310 43 51 80 88 0 2805 358 2447 .846 2595 2237 1.182 .79 -.241 -.34
5 1967 3164 208 265 1759 2899 1408 1056 215 280 1200 791 0 0 2305 5591 77 156 87 79 80 74 4658 1991 .607 1.648 .659 2.01 .97 4.25 70 370 1.61 .96 90 2870 6300 41 50 90 99 -100 4287 359 3928 2.233 1431 1072 .448 .893 1.159 -.163
6 3572 2450 211 261 3361 2189 3311 2107 219 283 3100 1846 0 0 1203 1202 74 158 100 100 100 100 5550 4946 1.535 .651 .595 .63 .61 .16 37 448 .69 .99 70 3050 6310 43 50 109 116 0 3319 354 2966 .882 2855 2501 1.133 .807 -.18 -.31
7 2406 1320 209 254 2197 1066 2379 1371 219 273 2170 1117 0 0 529 439 77 145 100 97 100 94 3263 3287 2.061 .485 .515 .49 .49 .18 70 340 .56 .98 90 3200 6310 42 51 123 132 0 1788 344 1444 .657 1858 1513 1.521 .697 -.605 -.52
8 3013 1833 213 271 2800 1562 2876 1720 216 290 2663 1449 0 0 728 744 74 144 100 100 100 100 4362 4112 1.793 .558 .544 .55 .55 .19 60 303 .62 .98 80 3320 6320 44 52 136 144 0 2483 367 2116 .756 2330 1963 1.323 .737 -.404 -.44
9 2103 4062 203 256 1900 3806 2083 4027 204 279 1880 3771 0 0 389 1148 68 159 100 100 100 100 5706 5651 .499 2.003 2.006 2.04 1.92 .63 80 290 1.95 .98 100 3470 6320 43 53 150 160 0 5503 347 5157 2.714 5456 5109 .368 2.718 1.44 1.442
10 3964 4749 195 241 3769 4508 3834 4087 203 271 3639 3846 0 0 883 2379 72 171 100 100 100 100 8277 7485 .836 1.196 1.057 1.15 1.11 .37 80 277 1.21 .97 100 3610 6320 43 53 164 174 0 6434 327 6108 1.621 5537 5211 .617 1.432 .696 .518
11 1728 1483 188 247 1540 1236 1715 1386 197 274 1527 1139 0 0 240 473 73 161 100 100 100 99 2776 2666 1.246 .803 .746 .81 .78 .35 69 366 .86 .98 90 3750 6310 42 51 178 187 0 2009 335 1675 1.087 1878 1543 .92 1.011 .121 .015
12 1957 1533 194 247 1763 1286 1994 1471 198 266 1800 1224 0 0 503 467 67 155 100 100 100 99 3049 3024 1.371 .729 .68 .76 .73 .34 69 379 .79 .99 90 3900 6320 43 52 193 202 0 2077 335 1742 .988 1993 1658 1.012 .921 -.017 -.118
13 3561 2559 190 236 3371 2323 3555 2626 196 265 3365 2390 0 0 689 777 65 160 100 100 100 100 5694 5755 1.451 .689 .71 .67 .68 .18 69 375 .72 .99 90 4050 6310 42 51 208 217 0 3467 320 3147 .934 3558 3238 1.071 .962 -.099 -.055
14 3906 8621 196 242 3710 8379 3666 6835 200 270 3470 6593 0 0 1029 4655 68 152 100 100 100 100 12089 10063 .443 2.258 1.9 2.15 2.04 .6 69 393 2.23 .98 90 4210 6310 42 51 224 233 0 11680 328 11352 3.06 9261 8933 .327 2.574 1.614 1.364
15 2135 2577 196 247 1939 2330 2118 2463 200 264 1922 2216 0 0 344 686 65 139 100 100 100 100 4269 4138 .832 1.202 1.153 1.22 1.2 .37 52 346 1.24 .98 80 4350 6320 44 52 239 247 0 3492 335 3157 1.628 3337 3002 .614 1.562 .703 .644
16 8406 5361 195 235 8211 5126 8300 5245 198 261 8105 5010 0 0 1241 1212 66 138 100 100 100 100 13337 13115 1.602 .624 .618 .61 .61 .11 70 367 .65 1 90 4510 6320 43 52 254 263 0 7263 318 6945 .846 7106 6788 1.182 .837 -.242 -.256
17 2945 2183 204 244 2741 1939 2872 2070 209 266 2668 1826 0 0 498 721 72 135 100 100 100 100 4680 4494 1.414 .707 .684 .7 .69 .24 70 324 .74 .99 90 4660 6310 42 51 269 278 0 2958 331 2627 .958 2805 2474 1.043 .927 -.061 -.109
18 4607 4069 202 256 4405 3813 4589 4023 210 272 4387 3767 0 0 496 950 69 144 100 100 100 100 8218 8154 1.155 .866 .859 .86 .88 .21 70 305 .88 .99 90 4800 6320 43 52 283 292 0 5513 347 5166 1.173 5451 5104 .853 1.163 .23 .218
19 11041 8816 199 256 10842 8560 10741 8367 202 276 10542 8111 0 0 1756 2545 68 155 100 100 100 100 19402 18653 1.267 .79 .769 .78 .75 .18 86 280 .81 .99 100 4940 6320 43 53 297 307 0 11945 347 11598 1.07 11336 10989 .935 1.042 .097 .06
20 2712 2643 192 274 2520 2369 2913 2707 197 283 2721 2433 0 0 550 718 69 146 100 100 100 100 4889 5154 1.064 .94 .894 .96 .94 .31 86 295 .99 .98 100 5090 6330 44 54 312 322 0 3581 371 3210 1.274 3668 3296 .785 1.211 .349 .277

Total number of rows: 41472

Table truncated, full table size 9449 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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