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Sample GSM48204 Query DataSets for GSM48204
Status Public on Apr 21, 2005
Title C-4-3
Sample type RNA
 
Channel 1
Source name cy3 Pool
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) [email protected]
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 �m 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 �m 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 �m 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 R� (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 R� (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 2220 3780 110 500 533 103 392 394 22 92 83 0 605 656 166 383 395 104 91 57 0 0.486 0.516 0.490 0.443 1.471 0.422 0.811 80 426 330 414 -1.040 108 222 141 273 42603 52501 6.318 2.510 0 0
2 2400 3780 110 6316 5843 1264 393 394 19 100 100 0 31726 29304 7036 381 397 208 100 100 0 0.189 0.188 0.189 0.188 1.076 0.186 0.991 80 442 37268 34373 -2.404 5923 31345 5450 28923 467422 2344315 286.789 138.976 0 0
3 2580 3790 100 3591 3402 659 392 393 19 100 100 0 4674 4552 798 381 393 202 100 100 0 0.745 0.722 0.730 0.716 1.123 0.722 0.983 80 426 7492 7181 -0.424 3199 4293 3010 4171 272186 364149 158.368 20.589 0 0
4 2760 3790 100 19846 19153 3738 391 392 11 100 100 0 20164 19783 4019 380 382 14 100 100 0 0.983 0.967 0.952 0.969 1.082 0.968 0.992 80 426 39239 38165 -0.024 19455 19784 18762 19403 1532262 1582626 1705.545 1385.786 0 0
5 2940 3790 110 1040 1001 179 391 392 11 100 100 0 1223 1179 221 380 382 14 100 100 0 0.770 0.763 0.761 0.760 1.129 0.761 0.972 80 476 1492 1409 -0.377 649 843 610 799 80057 94337 55.364 56.929 0 0
6 3130 3790 110 4783 4702 806 391 392 7 100 100 0 11953 11449 2291 380 381 8 100 100 0 0.380 0.389 0.386 0.391 1.086 0.388 0.992 80 462 15965 15380 -1.398 4392 11573 4311 11069 376139 915959 615.714 1383.500 0 0
7 3300 3790 110 8804 8990 2265 390 394 56 100 100 0 14397 14564 3607 379 387 113 100 100 0 0.600 0.606 0.606 0.602 1.125 0.606 0.992 80 462 22432 22785 -0.736 8414 14018 8600 14185 719208 1165131 153.500 125.460 0 0
8 3490 3800 100 590 590 50 391 391 7 100 100 0 759 752 69 379 382 34 100 100 0 0.524 0.534 0.531 0.523 1.219 0.534 0.945 80 440 579 572 -0.933 199 380 199 373 47169 60174 28.429 10.882 0 0
9 3670 3800 110 1463 1451 218 391 393 17 100 100 0 5452 5216 1087 381 385 59 100 100 0 0.211 0.219 0.220 0.220 1.138 0.213 0.974 80 450 6143 5895 -2.242 1072 5071 1060 4835 116076 417282 62.235 81.881 0 0
10 3850 3800 110 1007 1008 123 391 393 18 100 100 0 1971 1913 219 381 386 60 100 100 0 0.387 0.403 0.398 0.399 1.158 0.401 0.970 80 464 2206 2149 -1.368 616 1590 617 1532 80666 153076 34.167 25.450 0 0
11 4030 3800 100 4782 4663 724 392 394 24 100 100 0 5607 5379 797 380 383 19 100 100 0 0.840 0.854 0.853 0.853 1.069 0.854 0.992 80 409 9617 9270 -0.252 4390 5227 4271 4999 373064 430354 177.875 262.947 0 0
12 4210 3800 110 13958 13358 1631 391 392 7 100 100 0 26416 25324 3724 379 382 22 100 100 0 0.521 0.520 0.518 0.522 1.065 0.514 0.992 80 464 39604 37912 -0.940 13567 26037 12967 24945 1068668 2025917 1852.286 1133.727 0 0
13 4390 3800 110 1099 1082 143 390 391 6 100 100 0 3934 3817 684 378 380 21 100 100 0 0.199 0.201 0.203 0.201 1.190 0.197 0.961 80 464 4265 4131 -2.326 709 3556 692 3439 86573 305320 115.167 163.667 0 0
14 4570 3810 110 827 817 80 392 392 6 100 100 0 1185 1174 152 379 379 8 100 100 0 0.540 0.535 0.528 0.536 1.112 0.533 0.981 80 470 1241 1220 -0.890 435 806 425 795 65374 93896 70.833 99.375 0 0
15 4750 3800 110 1649 1562 291 391 391 6 100 100 0 2034 1918 357 379 380 7 100 100 0 0.760 0.761 0.761 0.753 1.122 0.761 0.982 80 464 2913 2710 -0.396 1258 1655 1171 1539 124961 153465 195.167 219.714 0 0
16 4930 3810 100 847 837 92 391 391 6 100 100 0 1373 1357 163 380 380 7 100 100 0 0.459 0.456 0.455 0.451 1.159 0.457 0.978 80 442 1449 1423 -1.123 456 993 446 977 66958 108544 74.333 139.571 0 0
17 5110 3810 100 7091 6863 2016 391 392 6 100 100 0 6983 6958 1799 379 380 10 100 100 0 1.015 0.984 0.986 0.969 1.099 0.999 0.990 80 409 13304 13051 0.021 6700 6604 6472 6579 549054 556651 1078.500 657.800 0 0
18 5290 3810 110 1254 1257 141 391 392 7 100 100 0 3130 3192 441 379 379 6 100 100 0 0.314 0.308 0.310 0.308 1.085 0.308 0.985 80 464 3614 3679 -1.673 863 2751 866 2813 100584 255337 123.571 468.833 0 0
19 5470 3810 110 574 578 43 391 391 7 100 100 0 772 774 60 379 379 6 100 100 0 0.466 0.473 0.465 0.466 1.212 0.475 0.946 80 464 576 582 -1.103 183 393 187 395 46202 61885 26.714 65.833 0 0
20 5650 3810 110 3502 3411 728 391 391 7 100 100 0 4137 3981 829 379 380 9 100 100 0 0.828 0.838 0.829 0.836 1.071 0.840 0.993 80 464 6869 6622 -0.273 3111 3758 3020 3602 272857 318440 431.429 400.111 0 0

Total number of rows: 17664

Table truncated, full table size 3493 Kbytes.




Supplementary data files not provided
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