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Sample GSM48184 Query DataSets for GSM48184
Status Public on Apr 21, 2005
Title C-2-5
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 1460 12320 100 837 904 352 49 68 105 100 100 0 508 554 201 42 47 38 100 100 0 1.691 1.670 1.612 1.662 1.255 1.732 0.863 80 396 1254 1367 0.758 788 466 855 512 72287 44280 7.962 13.342 -50 0
2 1640 12330 100 308 385 200 48 52 20 100 100 0 196 219 94 41 42 11 100 100 0 1.677 1.893 1.753 1.833 1.538 2.050 0.804 80 442 415 515 0.746 260 155 337 178 30803 17549 16.650 16.091 0 0
3 1820 12330 100 453 470 163 47 50 20 100 100 0 255 261 87 40 41 11 100 100 0 1.888 1.914 1.884 1.941 1.415 1.960 0.875 80 442 621 644 0.917 406 215 423 221 37593 20881 21.000 20.000 0 0
4 2000 12330 100 828 883 310 48 50 18 100 100 0 521 547 177 39 40 11 100 100 0 1.618 1.644 1.638 1.635 1.313 1.733 0.872 80 442 1262 1343 0.694 780 482 835 508 70645 43788 46.278 46.091 0 0
5 2180 12330 110 370 385 115 48 50 17 100 100 0 179 183 56 40 41 12 100 100 0 2.317 2.357 2.292 2.410 1.597 2.443 0.724 80 484 461 480 1.212 322 139 337 143 30772 14665 19.706 11.833 0 0
6 2360 12330 110 627 642 155 48 50 17 100 100 0 367 374 100 41 42 12 100 100 0 1.776 1.784 1.721 1.836 1.434 1.783 0.860 80 484 905 927 0.829 579 326 594 333 51364 29895 34.824 27.667 0 0
7 2540 12330 110 835 821 216 50 53 18 100 100 0 463 485 155 42 43 12 100 100 0 1.865 1.740 1.764 1.775 1.386 1.751 0.827 80 496 1206 1214 0.899 785 421 771 443 65714 38763 42.667 36.833 0 0
8 2720 12320 90 193 223 110 51 53 18 96 90 0 115 120 37 41 42 12 98 94 0 1.919 2.177 2.098 1.995 1.998 2.674 0.596 52 380 216 251 0.940 142 74 172 79 11582 6265 9.444 6.500 0 0
9 2900 12330 100 270 262 122 52 55 19 98 96 0 147 154 63 42 43 12 98 96 0 2.076 1.875 1.800 1.788 1.878 2.070 0.678 80 452 323 322 1.054 218 105 210 112 20947 12326 10.895 9.250 0 0
10 3080 12330 100 221 243 132 52 55 20 98 95 0 111 129 61 42 43 11 95 87 0 2.449 2.195 2.290 2.270 2.060 2.480 0.682 80 452 238 278 1.292 169 69 191 87 19435 10344 9.400 7.818 0 0
11 3270 12330 110 568 570 160 50 53 20 100 100 0 325 323 75 41 43 12 100 100 0 1.824 1.844 1.815 1.827 1.494 1.999 0.785 80 469 802 802 0.867 518 284 520 282 45618 25810 25.850 23.333 0 0
12 3440 12320 110 2025 1946 450 51 57 52 100 100 0 1089 1067 190 41 44 20 100 100 0 1.884 1.847 1.910 1.782 1.439 1.941 0.902 80 463 3022 2921 0.913 1974 1048 1895 1026 155719 85391 36.327 51.150 0 0
13 3620 12320 110 283 288 113 54 60 52 96 87 0 164 167 58 44 46 20 100 95 0 1.908 1.902 1.910 1.837 1.890 2.109 0.668 80 476 349 357 0.932 229 120 234 123 23050 13376 4.385 6.050 0 0
14 3800 12320 110 344 350 120 53 56 19 100 100 0 197 193 55 42 43 12 100 100 0 1.877 1.967 1.914 1.933 1.556 2.180 0.757 80 476 446 448 0.909 291 155 297 151 27983 15408 15.474 12.500 0 0
15 3980 12320 90 302 287 159 53 55 18 98 90 0 158 171 82 42 44 12 98 90 0 2.147 1.814 1.669 1.707 1.986 2.005 0.786 52 378 365 363 1.102 249 116 234 129 14931 8877 12.889 10.583 0 0
16 4160 12320 100 147 166 75 55 57 20 92 82 0 121 124 33 43 45 13 100 98 0 1.179 1.370 1.317 1.123 2.352 1.805 0.564 80 436 170 192 0.238 92 78 111 81 13290 9927 5.450 6.077 0 0
17 4340 12320 110 143 174 117 53 57 22 86 71 0 109 126 64 42 44 12 100 90 0 1.343 1.440 1.371 1.209 2.322 2.231 0.522 80 476 157 205 0.426 90 67 121 84 13893 10074 5.318 6.833 0 0
18 4520 12320 110 281 308 161 51 55 24 100 95 0 182 202 92 42 43 12 100 100 0 1.643 1.606 1.715 1.518 1.665 1.800 0.747 80 486 370 417 0.716 230 140 257 160 24653 16126 10.542 13.250 0 0
19 4720 12320 100 89 153 133 51 54 19 65 50 0 81 103 64 42 43 12 81 70 0 0.974 1.672 1.458 1.272 2.923 2.093 0.642 80 432 77 163 -0.037 38 39 102 61 12211 8226 5.211 5.000 0 0
20 4890 12320 110 250 256 79 50 54 24 100 100 0 182 188 43 43 45 15 100 100 0 1.439 1.421 1.381 1.380 1.508 1.511 0.759 80 488 339 351 0.525 200 139 206 145 20452 15001 8.417 9.533 0 0

Total number of rows: 17664

Table truncated, full table size 3089 Kbytes.




Supplementary data files not provided

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