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Sample GSM48206 Query DataSets for GSM48206
Status Public on Apr 21, 2005
Title C-4-5
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 1890 6790 100 79 93 41 42 42 6 96 87 0 208 239 78 59 59 9 100 100 0 0.248 0.283 0.272 0.229 1.786 0.317 0.783 80 420 186 231 -2.010 37 149 51 180 7445 19147 8.500 20.000 0 0
2 2070 6790 100 732 698 221 41 42 6 100 100 0 865 831 187 59 60 12 100 100 0 0.857 0.851 0.850 0.816 1.304 0.892 0.936 80 426 1497 1429 -0.222 691 806 657 772 55843 66440 109.333 64.250 0 0
3 2250 6790 100 284 289 91 42 47 62 93 93 0 505 502 88 59 62 22 100 100 0 0.543 0.558 0.552 0.508 1.543 0.578 0.888 80 426 688 690 -0.882 242 446 247 443 23082 40138 3.903 20.000 0 0
4 2430 6790 100 1281 1415 480 43 47 55 100 100 0 1470 1546 421 60 73 103 100 100 0 0.878 0.923 0.904 0.907 1.198 0.938 0.925 80 426 2648 2858 -0.188 1238 1410 1372 1486 113205 123669 24.873 14.301 0 0
5 2610 6790 100 270 271 80 42 50 69 98 88 0 457 459 74 61 74 104 100 100 0 0.576 0.575 0.574 0.551 1.328 0.603 0.879 80 426 624 627 -0.796 228 396 229 398 21718 36728 3.203 3.702 0 0
6 2790 6790 110 411 421 107 42 46 22 100 100 0 582 585 89 61 77 172 100 95 0 0.708 0.723 0.704 0.700 1.279 0.655 0.760 80 445 890 903 -0.498 369 521 379 524 33653 46765 17.045 2.953 0 0
7 2970 6790 100 574 568 181 42 44 19 98 97 0 738 738 156 59 71 147 100 98 0 0.784 0.775 0.780 0.709 1.583 0.799 0.903 80 426 1211 1205 -0.352 532 679 526 679 45473 59072 27.579 4.537 0 0
8 3150 6790 100 137 136 36 41 42 6 98 97 0 312 310 44 57 59 11 100 100 0 0.376 0.375 0.385 0.344 1.579 0.384 0.819 80 426 351 348 -1.409 96 255 95 253 10905 24832 15.667 22.818 0 0
9 3330 6790 110 328 327 79 42 49 59 100 97 0 468 473 101 59 169 1343 0 0 0 0.699 0.688 0.684 0.681 1.258 0.026 0.085 80 464 695 699 -0.516 286 409 285 414 26164 37820 4.712 0.226 0 0
10 3510 6800 110 96 97 20 42 46 47 67 3 0 265 264 30 59 88 283 0 0 0 0.262 0.268 0.268 0.252 1.548 0.258 0.762 80 471 260 260 -1.932 54 206 55 205 7787 21147 1.085 0.622 0 0
11 3690 6790 110 682 670 196 42 43 7 100 100 0 792 756 154 57 58 11 100 100 0 0.871 0.898 0.897 0.874 1.267 0.928 0.925 80 464 1375 1327 -0.200 640 735 628 699 53580 60446 89.571 63.455 0 0
12 3870 6790 110 1543 1570 476 42 42 6 100 100 0 1624 1636 411 57 58 10 100 100 0 0.958 0.968 0.959 0.934 1.297 0.990 0.961 80 464 3068 3107 -0.062 1501 1567 1528 1579 125607 130854 254.667 157.800 0 0
13 4050 6790 110 247 238 63 42 43 7 98 97 0 371 365 61 56 57 10 100 100 0 0.651 0.634 0.642 0.597 1.537 0.640 0.898 80 464 520 505 -0.620 205 315 196 309 19044 29170 27.857 30.800 0 0
14 4230 6790 110 232 230 49 42 42 6 100 100 0 359 351 49 55 56 10 100 100 0 0.625 0.635 0.662 0.619 1.317 0.645 0.911 80 464 494 484 -0.678 190 304 188 296 18417 28083 31.333 29.500 0 0
15 4410 6790 110 513 522 119 42 43 6 100 100 0 630 622 82 55 57 11 100 100 0 0.819 0.847 0.844 0.818 1.337 0.872 0.924 80 464 1046 1047 -0.288 471 575 480 567 41766 49795 79.833 51.364 0 0
16 4590 6800 110 134 134 34 42 42 6 100 100 0 359 350 63 55 57 10 100 100 0 0.303 0.312 0.307 0.299 1.426 0.302 0.830 80 484 396 387 -1.724 92 304 92 295 10738 27989 15.333 29.300 0 0
17 4770 6800 100 1596 1528 380 43 43 6 100 100 0 1460 1383 342 56 58 10 100 100 0 1.106 1.119 1.135 1.128 1.217 1.117 0.968 80 430 2957 2812 0.146 1553 1404 1485 1327 122228 110657 247.500 132.500 0 0
18 4950 6800 110 173 177 38 42 42 6 100 100 0 335 335 48 55 57 10 100 100 0 0.468 0.482 0.472 0.474 1.370 0.477 0.833 80 470 411 415 -1.096 131 280 135 280 14183 26768 22.500 27.800 0 0
19 5130 6800 100 112 113 27 43 43 6 100 100 0 245 247 52 56 57 10 100 100 0 0.365 0.366 0.356 0.352 1.410 0.333 0.766 80 442 258 261 -1.454 69 189 70 191 9040 19743 11.667 19.000 0 0
20 5310 6800 100 781 787 254 42 43 8 100 100 0 906 894 249 56 58 22 100 100 0 0.869 0.889 0.890 0.872 1.207 0.903 0.959 80 442 1589 1583 -0.202 739 850 745 838 62939 71495 93.000 38.000 0 0

Total number of rows: 17664

Table truncated, full table size 3248 Kbytes.




Supplementary data files not provided
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