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Sample GSM48207 Query DataSets for GSM48207
Status Public on Apr 21, 2005
Title C-4-6
Sample type RNA
 
Channel 1
Source name cy3 Liver3
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name cy5 Liver5
Organism Mus musculus
Extracted molecule total RNA
 
 
Description Each laboratory was provided with aliquots of two different RNA samples that were prepared in one of the Consortium laboratories - a sample prepared from mouse livers (Liver RNA), and a sample prepared from equal amounts of RNA isolated from five mouse tissues (liver, kidney, lung, brain and spleen: Pooled RNA).
 
Submission date Apr 13, 2005
Last update date May 27, 2005
Contact name Kenneth Lyon Phillips
E-mail(s) kphillips@icoria.com
Phone 919 425 3075
Organization name Paradigm Array Labs
Street address
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL1955
Series (1)
GSE2458 Cross-platform comparability of microarray data

Data table header descriptions
ID_REF
X the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength 1 (635 nm).
F635 Mean mean feature pixel intensity at wavelength 1 (635 nm).
F635 SD the standard deviation of the feature pixel intensity at wavelength 1 (635 nm).
B635 Median the median feature background intensity at wavelength 1 (635 nm).
B635 Mean the mean feature background intensity at wavelength 1 (635 nm).
B635 SD
% > B635+1SD
% > B635+2SD
F635 % Sat.
F532 Median median feature pixel intensity at wavelength 2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength 2 (532 nm).
F532 SD
B532 Median the median feature background intensity at wavelength 2 (532 nm).
B532 Mean the mean feature background intensity at wavelength 2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength 2 (532 nm).
% > B532+1SD
% > B532+2SD
F532 % Sat. the percentage of feature pixels at wavelength 2 that are saturated.
Ratio of Medians (635/532) the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R² (635/532) the coefficient of determination for the current regression value.
F Pixels the total number of feature pixels.
B Pixels the total number of background pixels.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
VALUE log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at wavelength 1 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at wavelength 2 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at wavelength 1 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at wavelength 2 with the median background subtracted.
F635 Total Intensity Total Intensity = the sum of feature pixel intensities at wavelength 1
F532 Total Intensity Total Intensity = the sum of feature pixel intensities at wavelength 1
SNR 635 the signal-to-noise ratio at wavelength 1, defined by (Mean Foreground 1- Mean Background 1) / (Standard deviation of Background 1)
SNR 532 the signal-to-noise ratio at wavelength 1, defined by (Mean Foreground 1- Mean Background 1) / (Standard deviation of Background 1)
Flags the type of flag associated with a feature.
Normalize the normalization status of the feature (included/not included).

Data table
ID_REF X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R² (635/532) F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize
1 1570 3820 90 708 721 128 445 446 18 100 100 0 866 890 131 409 411 12 100 100 0 0.575 0.574 0.559 0.528 1.348 0.598 0.906 52 366 720 757 -0.797 263 457 276 481 37469 46290 15.278 39.917 0 0
2 1750 3830 100 2897 2837 818 447 453 63 100 100 0 2251 2218 487 409 412 22 100 100 0 1.330 1.321 1.341 1.287 1.195 1.362 0.975 80 440 4292 4199 0.412 2450 1842 2390 1809 226974 177471 37.841 82.091 0 0
3 1930 3830 100 1476 1466 508 446 464 178 97 95 0 1441 1517 736 409 454 608 87 27 0 0.998 0.921 0.971 0.931 1.286 0.835 0.898 80 430 2062 2128 -0.003 1030 1032 1020 1108 117272 121322 5.629 1.748 0 0
4 2110 3820 110 7761 6969 2181 445 458 161 100 100 0 5240 4771 1405 409 449 586 100 96 0 1.514 1.496 1.490 1.486 1.111 1.519 0.991 80 464 12147 10886 0.599 7316 4831 6524 4362 557540 381683 40.441 7.375 0 0
5 2290 3830 100 1624 1514 392 446 450 27 100 100 0 1462 1409 280 406 408 11 100 100 0 1.116 1.065 1.050 1.023 1.217 1.102 0.954 80 430 2234 2071 0.158 1178 1056 1068 1003 121154 112706 39.407 91.000 0 0
6 2470 3830 110 1579 1521 327 446 449 18 100 100 0 1462 1409 230 408 410 15 100 100 0 1.075 1.074 1.071 1.043 1.195 1.099 0.969 80 471 2187 2076 0.104 1133 1054 1075 1001 121700 112712 59.556 66.600 0 0
7 2650 3820 110 2363 2311 652 445 450 53 100 100 0 1888 1826 468 407 410 22 100 100 0 1.295 1.315 1.318 1.310 1.152 1.344 0.973 80 476 3399 3285 0.373 1918 1481 1866 1419 184905 146111 35.113 64.364 0 0
8 2830 3830 100 685 683 70 445 450 46 98 97 0 915 894 96 408 410 24 100 100 0 0.473 0.490 0.497 0.476 1.262 0.509 0.813 80 430 747 724 -1.079 240 507 238 486 54606 71553 5.065 20.167 0 0
9 3010 3820 110 1679 1555 297 447 451 27 100 100 0 1453 1400 224 406 409 14 100 100 0 1.177 1.115 1.122 1.117 1.259 1.125 0.963 80 464 2279 2102 0.235 1232 1047 1108 994 124384 111963 40.889 70.786 0 0
10 3190 3830 110 647 649 64 448 450 21 100 100 0 884 873 59 406 408 13 100 100 0 0.416 0.430 0.433 0.410 1.405 0.440 0.851 80 471 677 668 -1.264 199 478 201 467 51906 69805 9.476 35.769 0 0
11 3370 3820 100 3448 3258 859 448 448 13 100 100 0 2537 2402 484 406 408 13 100 100 0 1.408 1.408 1.421 1.375 1.167 1.444 0.979 80 426 5131 4806 0.493 3000 2131 2810 1996 260613 192192 216.154 153.385 0 0
12 3550 3820 100 4408 4136 1145 446 446 14 100 100 0 3222 3086 730 406 408 13 100 100 0 1.407 1.377 1.385 1.354 1.144 1.394 0.985 80 426 6778 6370 0.493 3962 2816 3690 2680 330882 246841 263.571 206.000 0 0
13 3730 3820 110 1177 1166 190 443 445 20 100 100 0 1166 1155 134 404 407 17 100 100 0 0.963 0.963 0.959 0.943 1.213 0.980 0.955 80 464 1496 1474 -0.054 734 762 723 751 93278 92415 36.050 44.000 0 0
14 3910 3820 100 1061 1056 155 443 445 20 100 100 0 1072 1061 100 404 406 17 100 100 0 0.925 0.933 0.929 0.910 1.223 0.953 0.949 80 426 1286 1270 -0.112 618 668 613 657 84516 84894 30.550 38.529 0 0
15 4090 3820 100 1851 1761 388 445 446 14 100 100 0 1550 1485 220 403 405 13 100 100 0 1.226 1.216 1.298 1.186 1.309 1.253 0.932 80 436 2553 2398 0.294 1406 1147 1316 1082 140882 118830 93.929 83.077 0 0
16 4280 3820 100 796 819 117 445 445 13 100 100 0 1018 998 96 404 405 13 100 100 0 0.572 0.630 0.603 0.605 1.243 0.654 0.940 80 424 965 968 -0.807 351 614 374 594 65502 79835 28.769 45.615 0 0
17 4450 3820 100 7977 7421 2244 445 450 54 100 100 0 4915 4690 1346 402 407 54 100 100 0 1.669 1.627 1.624 1.623 1.112 1.631 0.987 80 424 12045 11264 0.739 7532 4513 6976 4288 593672 375208 129.093 79.315 0 0
18 4640 3820 100 872 863 101 445 447 21 100 100 0 977 973 66 402 405 43 100 100 0 0.743 0.732 0.732 0.711 1.290 0.754 0.923 80 436 1002 989 -0.429 427 575 418 571 69076 77854 19.810 13.209 0 0
19 4820 3820 100 799 794 77 446 448 28 100 100 0 902 893 51 402 404 15 100 100 0 0.706 0.709 0.720 0.695 1.210 0.717 0.946 80 426 853 839 -0.502 353 500 348 491 63510 71401 12.357 32.600 0 0
20 5000 3820 100 3414 3944 1535 446 446 13 100 100 0 2551 2842 921 403 404 13 100 100 0 1.382 1.434 1.434 1.394 1.141 1.476 0.984 80 426 5116 5937 0.466 2968 2148 3498 2439 315503 227343 269.077 187.538 0 0

Total number of rows: 17664

Table truncated, full table size 3452 Kbytes.




Supplementary data files not provided
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