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Sample GSM48185 Query DataSets for GSM48185
Status Public on Apr 21, 2005
Title C-2-6
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 1450 12800 100 774 875 439 45 51 46 100 100 0 518 595 308 43 46 35 100 100 0 1.535 1.504 1.515 1.534 1.335 1.997 0.740 80 428 1204 1382 0.618 729 475 830 552 70022 47595 17.913 15.686 0 0
2 1630 12790 90 513 808 685 45 49 25 98 98 0 419 514 343 43 45 13 100 100 0 1.245 1.620 1.589 1.363 1.912 1.870 0.860 52 379 844 1234 0.316 468 376 763 471 41995 26703 30.360 36.077 0 0
3 1800 12790 90 1515 1542 872 46 48 16 100 100 0 1005 911 413 42 43 12 100 100 0 1.525 1.722 1.714 1.550 1.692 1.910 0.850 52 379 2432 2365 0.609 1469 963 1496 869 80168 47377 93.375 72.333 0 0
4 1980 12800 100 768 1232 1142 45 47 15 100 100 0 569 674 553 42 42 11 100 98 0 1.372 1.878 1.834 1.738 1.761 2.055 0.878 80 452 1250 1819 0.456 723 527 1187 632 98559 53882 79.000 57.455 0 0
5 2160 12800 100 1237 1453 718 44 47 18 100 100 0 769 793 352 40 42 11 100 100 0 1.636 1.871 1.867 1.900 1.445 1.979 0.871 80 442 1922 2162 0.711 1193 729 1409 753 116202 63447 78.111 68.273 0 0
6 2340 12800 100 902 999 554 43 46 18 100 100 0 508 562 296 41 42 11 98 98 0 1.839 1.835 1.740 1.907 1.532 1.881 0.860 80 452 1326 1477 0.879 859 467 956 521 79955 44998 52.944 47.273 0 0
7 2520 12790 90 1034 1146 525 43 47 21 100 100 0 559 664 303 41 42 13 100 100 0 1.913 1.770 1.790 1.777 1.312 1.759 0.894 52 387 1509 1726 0.936 991 518 1103 623 59603 34505 52.333 47.846 0 0
8 2700 12790 90 619 701 387 45 47 16 100 100 0 349 420 200 41 43 13 100 100 0 1.864 1.731 1.613 1.715 1.419 0.195 0.290 52 393 882 1035 0.898 574 308 656 379 36469 21836 40.875 29.000 0 0
9 2880 12800 100 519 799 614 45 47 15 100 100 0 323 460 359 43 44 14 97 96 0 1.693 1.808 1.816 2.019 1.867 1.777 0.905 80 462 754 1171 0.759 474 280 754 417 63948 36760 50.133 29.714 0 0
10 3060 12790 90 521 630 464 46 48 15 100 100 0 326 360 212 42 43 12 100 100 0 1.673 1.836 1.710 1.591 1.775 2.020 0.763 52 380 759 902 0.742 475 284 584 318 32770 18729 38.800 26.417 0 0
11 3240 12800 100 1067 1156 627 45 48 17 100 100 0 652 667 367 44 45 12 100 98 0 1.681 1.783 1.708 1.959 1.716 1.796 0.864 80 452 1630 1734 0.749 1022 608 1111 623 92514 53355 65.176 51.833 0 0
12 3410 12790 90 579 677 311 43 47 18 100 100 0 355 384 174 43 45 13 100 100 0 1.718 1.859 1.838 1.886 1.497 2.011 0.804 52 371 848 975 0.781 536 312 634 341 35225 19986 35.000 26.077 0 0
13 3600 12800 100 471 521 261 46 49 17 100 100 0 320 335 180 42 45 13 100 98 0 1.529 1.621 1.622 1.737 1.724 1.653 0.782 80 449 703 768 0.612 425 278 475 293 41667 26780 27.765 22.308 0 0
14 3780 12790 110 643 721 515 46 50 21 100 96 0 357 416 253 43 45 12 100 100 0 1.901 1.810 1.888 1.623 1.855 1.940 0.833 80 488 911 1048 0.927 597 314 675 373 57685 33289 31.952 30.917 0 0
15 3960 12790 80 307 428 360 45 48 17 98 94 0 218 257 170 46 46 12 100 98 0 1.523 1.815 1.633 1.667 1.875 2.087 0.807 52 328 434 594 0.607 262 172 383 211 22249 13342 22.353 17.583 0 0
16 4130 12790 90 106 148 89 46 47 16 94 88 0 95 118 62 43 45 12 96 88 0 1.154 1.360 1.351 1.337 1.876 1.546 0.681 52 386 112 177 0.206 60 52 102 75 7685 6131 6.313 6.083 0 0
17 4320 12790 100 142 236 196 47 49 18 96 91 0 112 155 96 43 45 12 97 92 0 1.377 1.688 1.709 1.416 2.378 1.998 0.698 80 454 164 301 0.461 95 69 189 112 18851 12363 10.389 9.167 0 0
18 4500 12790 100 156 223 173 46 48 16 96 95 0 111 148 95 42 43 12 97 92 0 1.594 1.670 1.484 1.651 2.373 1.947 0.618 80 436 179 283 0.673 110 69 177 106 17834 11820 10.938 8.750 0 0
19 4680 12790 100 221 336 313 46 48 18 98 97 0 150 188 123 40 42 12 100 98 0 1.591 1.959 1.812 1.653 1.959 2.354 0.697 80 436 285 438 0.670 175 110 290 148 26847 15058 16.000 12.167 0 0
20 4870 12790 100 133 150 82 44 47 17 91 86 0 103 117 55 41 43 12 98 88 0 1.435 1.395 1.431 1.299 2.251 1.538 0.647 80 424 151 182 0.522 89 62 106 76 11972 9332 6.059 6.167 0 0

Total number of rows: 17664

Table truncated, full table size 3085 Kbytes.




Supplementary data files not provided
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