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Sample GSM48210 Query DataSets for GSM48210
Status Public on Apr 21, 2005
Title C-5-1
Sample type RNA
 
Channel 1
Source name cy3 Liver3
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name cy5 Pool
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 1650 7180 90 30131 30800 12650 1072 2074 2655 100 98 0 11221 12927 7015 1569 2560 2768 86 78 0 3.011 2.617 2.388 2.785 2.552 3.330 0.310 52 377 38711 41086 1.590 29059 9652 29728 11358 1601578 672207 10.820 3.745 0 0
2 1830 7190 100 21680 23391 10760 809 1839 2493 100 97 0 10620 11713 5822 1942 2680 2817 93 76 0 2.405 2.311 2.623 2.277 2.168 2.927 0.324 80 462 29549 32353 1.266 20871 8678 22582 9771 1871274 937014 8.645 3.207 0 0
3 2010 7180 90 17923 19449 10281 913 2055 2652 98 90 0 10072 10632 4836 1614 2571 2834 90 76 0 2.011 2.055 2.186 2.057 2.597 2.920 0.196 52 379 25468 27554 1.008 17010 8458 18536 9018 1011342 552848 6.559 2.844 0 0
4 2190 7180 100 20176 26044 19661 1025 2128 3567 93 82 6 13741 14551 7965 1418 2811 5074 87 56 0 1.554 1.905 1.577 1.626 2.809 3.095 0.265 80 446 31474 38152 0.636 19151 12323 25019 13133 2083496 1164117 6.705 2.314 0 0
5 2370 7180 100 15301 19492 14009 921 1882 2302 96 87 0 13312 14047 6973 1997 2917 3131 90 78 0 1.271 1.541 1.573 1.355 3.279 2.299 0.253 80 436 25695 30621 0.346 14380 11315 18571 12050 1559332 1123772 7.650 3.555 0 0
6 2550 7180 100 10673 13513 10220 939 2159 2863 92 75 0 14436 17014 8753 2986 3617 3254 93 80 0 0.850 0.896 0.877 0.823 3.589 0.819 0.152 80 446 21184 26602 -0.234 9734 11450 12574 14028 1081074 1361129 3.966 4.117 0 0
7 2740 7180 100 14953 16397 9969 815 1928 2667 93 86 0 25197 25362 10022 5803 8497 8456 87 55 0 0.729 0.797 0.704 0.720 2.869 0.546 0.218 80 442 33532 35141 -0.456 14138 19394 15582 19559 1311799 2028936 5.425 1.994 0 0
8 2910 7190 110 7388 9965 8024 893 1866 2415 81 62 0 45151 45731 14308 9424 11044 7916 98 93 21 0.182 0.250 0.201 0.185 2.976 0.175 0.257 80 484 42222 45379 -2.460 6495 35727 9072 36307 797211 3658473 3.354 4.382 0 0
9 3080 7170 90 20387 23196 13215 962 2079 2713 94 90 0 20652 23224 11989 7471 9497 8047 73 38 1 1.474 1.411 1.646 1.325 3.962 1.805 0.019 52 373 32606 37987 0.559 19425 13181 22234 15753 1206172 1207669 7.784 1.706 0 0
10 3270 7200 90 19316 18970 10257 875 1887 2438 94 90 0 16361 16826 6436 2774 4348 4964 90 75 0 1.357 1.288 1.279 1.271 2.666 1.183 0.217 52 386 32028 32147 0.441 18441 13587 18095 14052 986436 874930 7.007 2.514 0 0
11 3450 7180 100 30606 33683 18460 878 1856 2404 97 96 7 16659 16997 6843 2002 2966 3285 98 91 0 2.028 2.188 2.117 1.905 2.336 2.733 0.545 80 447 44385 47800 1.020 29728 14657 32805 14995 2694644 1359766 13.239 4.271 0 0
12 3640 7180 100 17435 20579 13951 856 1739 2156 96 91 0 13259 13942 6686 1428 2290 2607 96 85 0 1.401 1.576 1.573 1.384 3.225 2.273 0.272 80 424 28410 32237 0.487 16579 11831 19723 12514 1646311 1115361 8.738 4.470 0 0
13 3810 7170 100 17711 18931 12191 800 1774 2438 92 85 0 12208 14042 7338 1368 2285 2666 95 87 0 1.560 1.431 1.634 1.267 3.122 1.797 0.275 80 404 27751 30805 0.642 16911 10840 18131 12674 1514504 1123398 7.037 4.410 0 0
14 3990 7170 110 19422 20374 13289 794 1801 2491 93 83 0 13766 14744 9149 1254 2209 2535 93 83 0 1.489 1.451 1.536 1.361 3.782 1.717 0.213 80 454 31140 33070 0.574 18628 12512 19580 13490 1629925 1179488 7.456 4.945 0 0
15 4170 7170 100 23499 22860 14491 639 1618 2316 91 87 0 13604 16110 9688 929 1909 2297 98 95 0 1.804 1.464 1.636 1.338 3.326 2.027 0.223 80 416 35535 37402 0.851 22860 12675 22221 15181 1828788 1288769 9.172 6.182 0 0
16 4350 7170 110 15426 18274 12332 956 1927 2455 96 88 0 13154 14426 8087 976 2026 2490 95 93 0 1.188 1.288 1.268 1.301 2.940 1.701 0.188 80 466 26648 30768 0.249 14470 12178 17318 13450 1461919 1154112 6.659 4.980 0 0
17 4530 7170 90 46014 44568 16008 701 1966 2695 100 98 13 17192 17044 6784 1473 2394 2865 98 94 0 2.883 2.817 2.880 2.861 1.957 3.268 0.364 52 373 61032 59438 1.527 45313 15719 43867 15571 2317520 886290 15.808 5.113 0 0
18 4710 7180 100 12844 16482 12683 479 1725 2735 90 80 0 10956 12435 6647 1434 2462 3088 92 75 0 1.299 1.455 1.408 1.243 3.032 1.728 0.185 80 436 21887 27004 0.377 12365 9522 16003 11001 1318537 994809 5.396 3.230 0 0
19 4890 7170 100 10370 13136 10693 724 1552 2021 85 75 0 9393 10707 6774 1196 2105 2639 90 72 0 1.177 1.305 1.274 1.124 3.947 2.050 0.097 80 426 17843 21923 0.235 9646 8197 12412 9511 1050894 856526 5.732 3.260 0 0
20 5080 7170 100 7326 8834 7106 767 1750 2280 81 65 0 11073 11382 5478 930 1998 2327 97 83 0 0.647 0.772 0.705 0.727 3.148 0.574 0.118 80 426 16702 18519 -0.629 6559 10143 8067 10452 706710 910535 3.107 4.033 0 0

Total number of rows: 17664

Table truncated, full table size 3630 Kbytes.




Supplementary data files not provided
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