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Sample GSM229023 Query DataSets for GSM229023
Status Public on Feb 24, 2012
Title shgc157|PR00254 Lemur
Sample type genomic
 
Channel 1
Source name Normal human female genomic DNA
Organism Homo sapiens
Characteristics Normal human female genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Lemur genomic DNA
Organism Lemur sp.
Characteristics Lemur 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) 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 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 1906 1809 200 391 1706 1418 1899 1567 240 429 1699 1176 0 0 726 995 665 276 93 96 70 84 3124 2875 1.203 .831 .692 1.11 .74 2.1 69 437 .96 .97 90 2270 5770 40 49 30 39 0 2526 546 1980 1.161 2188 1642 .862 .967 .215 -.049
2 2299 2162 207 374 2092 1788 2139 1990 254 444 1932 1616 0 0 933 1195 734 314 95 93 78 90 3880 3548 1.17 .855 .836 .88 .84 .51 60 357 .97 .97 80 2430 5780 42 50 47 55 0 3019 522 2497 1.193 2779 2257 .838 1.168 .255 .224
3 2498 1572 209 403 2289 1169 2281 1460 216 471 2072 1057 0 0 972 854 69 305 100 90 100 73 3458 3129 1.958 .511 .51 .55 .48 .46 60 363 .64 .95 80 2560 5780 42 50 60 68 0 2195 563 1632 .713 2039 1476 1.402 .712 -.488 -.489
4 2289 1794 211 431 2078 1363 2129 1723 218 491 1918 1292 0 0 847 1091 71 317 100 92 100 83 3441 3210 1.525 .656 .674 1.06 .59 3.07 52 360 .77 .93 80 2710 5780 42 50 75 83 0 2505 602 1903 .916 2406 1804 1.092 .941 -.127 -.088
5 876 1023 206 428 670 595 951 974 215 490 745 546 0 0 363 495 70 321 90 67 85 44 1265 1291 1.126 .888 .733 1.8 .83 3.84 79 350 1.2 .91 100 2840 5790 42 52 87 97 0 1429 598 831 1.24 1360 762 .806 1.023 .31 .033
6 2374 2111 209 409 2165 1702 2238 1938 214 477 2029 1529 0 0 980 1150 67 325 100 96 100 85 3867 3558 1.272 .786 .754 .81 .75 .54 52 381 .9 .98 80 3010 5780 42 50 105 113 0 2948 571 2377 1.098 2706 2135 .911 1.052 .135 .074
7 1952 1325 224 442 1728 883 1978 1244 226 502 1754 802 0 0 259 428 70 290 100 93 100 74 2611 2556 1.957 .511 .457 .51 .44 .28 70 319 .7 .96 90 3150 5780 41 50 118 127 0 1850 617 1233 .714 1737 1120 1.401 .638 -.487 -.647
8 2196 1567 225 452 1971 1115 2024 1434 241 548 1799 982 0 0 576 773 204 718 100 72 100 25 3086 2781 1.768 .566 .546 .6 .52 .5 60 319 .72 .97 80 3280 5780 42 50 132 140 0 2188 631 1557 .79 2002 1371 1.266 .762 -.34 -.392
9 1743 2501 225 454 1518 2047 1742 2427 243 547 1517 1973 0 0 301 872 208 736 100 97 100 77 3565 3490 .742 1.348 1.301 1.38 1.35 .59 70 306 1.42 .98 90 3420 5790 42 51 145 154 0 3492 634 2858 1.883 3389 2755 .531 1.816 .913 .861
10 3022 5016 230 445 2792 4571 3046 4915 231 485 2816 4470 0 0 912 1581 71 295 100 100 100 99 7363 7286 .611 1.637 1.587 1.82 1.59 1.12 80 276 1.64 .99 100 3560 5790 42 52 159 169 0 7004 621 6383 2.286 6863 6242 .437 2.217 1.193 1.148
11 1425 2771 240 454 1185 2317 1457 2645 244 510 1217 2191 0 0 297 827 72 504 100 100 99 97 3502 3408 .511 1.955 1.8 2.3 1.96 2.48 70 360 1.92 .98 90 3710 5780 41 50 174 183 0 3869 634 3235 2.73 3693 3060 .366 2.514 1.449 1.33
12 1723 2275 258 488 1465 1787 1779 2318 277 586 1521 1830 0 0 387 818 232 573 99 91 97 81 3252 3351 .82 1.22 1.203 1.27 1.2 .66 69 373 1.35 .98 90 3860 5780 41 50 189 198 0 3177 681 2495 1.703 3237 2555 .587 1.68 .768 .749
13 2858 5690 277 525 2581 5165 2815 5606 308 607 2538 5081 0 0 488 1811 259 437 100 99 100 99 7746 7619 .5 2.001 2.002 2.02 2.13 .72 70 351 2.02 .98 90 4000 5780 41 50 203 212 0 7946 733 7212 2.794 7828 7095 .358 2.796 1.483 1.483
14 3277 4939 263 526 3014 4413 2876 4759 295 617 2613 4233 0 0 1895 1682 285 424 100 100 100 99 7427 6846 .683 1.464 1.62 1.56 1.59 .45 80 353 1.53 .97 100 4180 5780 41 51 221 231 0 6897 735 6162 2.045 6645 5911 .489 2.262 1.032 1.178
15 1249 1732 240 482 1009 1250 1547 1843 285 502 1307 1361 0 0 780 919 437 286 64 75 61 70 2259 2668 .807 1.239 1.041 2.14 1.3 3.7 84 300 1.38 .97 100 4330 5780 41 51 236 246 0 2419 673 1746 1.73 2574 1901 .578 1.454 .791 .54
16 6795 10162 237 440 6558 9722 6811 10360 279 502 6574 9920 0 0 1586 2199 431 302 100 100 100 100 16280 16494 .675 1.482 1.509 1.54 1.45 .47 70 327 1.5 .99 90 4470 5780 41 50 250 259 0 14190 614 13576 2.07 14467 13852 .483 2.107 1.05 1.075
17 2730 3735 233 463 2497 3272 2829 3668 240 512 2596 3205 0 0 493 921 120 304 100 100 100 100 5769 5801 .763 1.31 1.235 1.35 1.23 .47 69 335 1.37 .99 90 4610 5780 41 50 264 273 0 5216 647 4569 1.83 5122 4475 .547 1.724 .872 .786
18 3482 6427 222 468 3260 5959 3718 6286 227 518 3496 5818 0 0 1052 1739 67 370 99 100 99 100 9219 9314 .547 1.828 1.664 2.52 1.89 4.15 80 293 1.81 .99 100 4760 5790 42 52 279 289 0 8975 654 8321 2.553 8778 8124 .392 2.324 1.352 1.217
19 8063 6290 202 496 7861 5794 8016 5970 212 563 7814 5474 0 0 1753 2064 71 470 100 99 100 99 13655 13288 1.357 .737 .701 .81 .7 .74 97 294 .79 .98 110 4900 5780 40 51 292 303 0 8783 693 8091 1.029 8337 7644 .972 .978 .042 -.032
20 2021 2795 202 456 1819 2339 2034 2667 210 495 1832 2211 0 0 359 1250 71 270 100 99 100 94 4158 4043 .778 1.286 1.207 1.28 1.16 .65 86 296 1.41 .97 100 5050 5790 42 52 308 318 0 3903 637 3266 1.796 3724 3087 .557 1.685 .844 .753

Total number of rows: 41472

Table truncated, full table size 9422 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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