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Sample GSM48214 Query DataSets for GSM48214
Status Public on Apr 21, 2005
Title C-5-5
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 1690 7120 90 25171 25398 7916 401 1400 2077 100 100 0 29193 28999 11215 315 1270 2029 100 100 0 0.858 0.871 0.898 0.908 1.814 0.796 0.555 52 384 53648 53681 -0.221 24770 28878 24997 28684 1320686 1507960 11.554 13.666 0 0
2 1860 7120 90 5560 6549 5593 250 1216 1971 84 57 0 7728 9263 8690 302 1271 2031 86 76 0 0.715 0.703 0.710 0.746 3.559 1.087 0.427 52 380 12736 15260 -0.484 5310 7426 6299 8961 340550 481675 2.706 3.935 0 0
3 2050 7120 100 5936 7626 6070 293 1251 1967 80 65 0 8584 9138 5942 48 986 1731 91 83 0 0.661 0.807 0.856 0.806 2.553 0.853 0.300 80 454 14179 16423 -0.597 5643 8536 7333 9090 610085 731075 3.241 4.709 0 0
4 2230 7120 90 6517 6991 5106 245 1252 1948 80 65 0 7642 8771 4946 36 1000 1784 98 88 0 0.825 0.772 0.667 0.694 2.983 0.651 0.194 52 386 13878 15481 -0.278 6272 7606 6746 8735 363547 456107 2.946 4.356 0 0
5 2410 7110 90 10832 10876 5574 421 1350 2100 96 86 0 9525 11664 6428 3 956 1720 100 96 0 1.093 0.897 0.929 0.845 2.520 0.868 0.302 52 375 19933 22116 0.129 10411 9522 10455 11661 565527 606520 4.536 6.226 0 0
6 2590 7120 100 4266 5300 4285 440 1395 2195 66 47 0 6291 6696 4048 0 784 1681 91 76 0 0.608 0.726 0.712 0.588 4.050 0.794 0.132 80 434 10117 11556 -0.717 3826 6291 4860 6696 424014 535683 1.779 3.517 0 0
7 2770 7120 90 4543 5533 4162 107 1180 1984 76 55 0 10847 10613 5638 53 1089 1795 96 88 0 0.411 0.514 0.424 0.465 3.381 0.340 0.122 52 372 15230 15986 -1.283 4436 10794 5426 10560 287710 551864 2.194 5.306 0 0
8 2950 7120 100 2797 3724 3442 111 1185 1930 56 42 0 5376 5894 4103 24 948 1629 85 66 0 0.502 0.616 0.614 0.599 4.791 0.376 0.060 80 434 8038 9483 -0.995 2686 5352 3613 5870 297891 471513 1.316 3.036 0 0
9 3130 7110 80 11624 12475 7421 136 1267 2102 96 90 0 11714 12174 6602 125 999 1670 98 94 0 0.991 1.024 1.125 0.989 2.209 1.073 0.355 52 328 23077 24388 -0.013 11488 11589 12339 12049 648699 633049 5.332 6.692 0 0
10 3310 7100 90 3608 4698 4303 147 1156 1762 69 50 0 7464 7468 3972 45 1148 2252 96 71 0 0.467 0.613 0.697 0.626 3.033 0.495 0.136 52 375 10880 11974 -1.100 3461 7419 4551 7423 244274 388359 2.010 2.806 0 0
11 3490 7110 100 7466 8281 6106 175 1130 1859 85 70 0 6906 8516 6261 99 894 1543 93 80 0 1.071 0.963 0.885 0.912 3.243 0.987 0.248 80 464 14098 16523 0.099 7291 6807 8106 8417 662486 681289 3.847 4.940 0 0
12 3680 7110 90 4295 4922 3994 144 1127 1865 73 51 0 6153 7441 4646 21 845 1628 92 80 0 0.677 0.644 0.568 0.659 2.541 0.626 0.158 52 378 10283 12198 -0.563 4151 6132 4778 7420 255962 386952 2.035 4.052 0 0
13 3850 7110 80 6961 7877 4533 159 1195 1872 92 84 0 7208 8174 5086 103 1011 1720 92 82 0 0.957 0.956 0.834 0.946 2.738 0.946 0.253 52 322 13907 15789 -0.063 6802 7105 7718 8071 409614 425045 3.569 4.165 0 0
14 4030 7110 110 8674 9596 7541 247 1298 2153 82 68 0 7820 9003 6009 48 906 1587 92 83 0 1.084 1.044 0.925 0.915 3.778 1.305 0.188 80 488 16199 18304 0.117 8427 7772 9349 8955 767692 720256 3.854 5.102 0 0
15 4210 7100 110 11192 11212 6687 247 1271 2093 92 78 0 11036 11535 6438 19 904 1627 97 91 0 0.993 0.952 1.030 0.890 3.048 0.970 0.393 80 454 21962 22481 -0.009 10945 11017 10965 11516 896956 922764 4.750 6.534 0 0
16 4390 7100 90 6502 7556 4968 337 1335 2014 82 67 0 6812 7082 4062 74 995 1801 90 76 0 0.915 1.030 0.937 0.890 3.372 1.218 0.106 52 374 12903 14227 -0.128 6165 6738 7219 7008 392898 368262 3.089 3.380 0 0
17 4580 7100 100 4963 6167 4983 97 987 1666 81 66 0 8040 8177 5243 112 1116 1893 92 75 0 0.614 0.753 0.774 0.733 3.535 0.620 0.129 80 441 12794 14135 -0.704 4866 7928 6070 8065 493381 654179 3.109 3.730 0 0
18 4760 7100 100 5184 6798 6117 247 1309 2003 78 61 0 6333 8425 6478 22 985 1711 90 73 0 0.782 0.780 0.902 0.736 3.561 0.582 0.084 80 426 11248 14954 -0.354 4937 6311 6551 8403 543800 673991 2.740 4.348 0 0
19 4930 7090 90 4506 5293 4050 227 1210 1893 75 57 0 7169 7554 4878 131 1150 2061 88 73 0 0.608 0.682 0.628 0.599 3.388 0.585 0.200 52 366 11317 12489 -0.718 4279 7038 5066 7423 275231 392806 2.157 3.107 0 0
20 5120 7100 100 4136 4990 4414 284 1191 1809 68 52 0 7509 7988 4699 201 1079 1791 91 80 0 0.527 0.604 0.636 0.649 3.862 0.463 0.074 80 445 11160 12493 -0.924 3852 7308 4706 7787 399186 639048 2.100 3.858 0 0

Total number of rows: 17664

Table truncated, full table size 3576 Kbytes.




Supplementary data files not provided

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