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Sample GSM48226 Query DataSets for GSM48226
Status Public on Apr 21, 2005
Title C-7-1
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 14, 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 2100 4510 100 43 88 130 0 179 1649 0 0 0 0 100 319 0 102 531 3 1 0 100000.000 0.880 0.955 0.707 5.259 0.254 0.238 80 380 43 188 16.610 43 0 88 100 7071 7996 -0.055 -0.004 -50 0
2 2280 4510 100 4144 4141 1018 0 189 1625 100 78 0 897 1024 839 0 137 656 68 22 0 4.620 4.044 4.948 4.898 1.956 3.943 0.209 80 394 5041 5165 2.208 4144 897 4141 1024 331302 81906 2.432 1.352 -50 0
3 2450 4510 110 728 714 338 0 74 252 92 66 0 663 764 642 0 104 554 58 21 0 1.098 0.935 1.042 1.030 1.943 0.551 0.125 80 440 1391 1478 0.135 728 663 714 764 57101 61103 2.540 1.191 0 0
4 2640 4510 100 2639 2656 821 0 47 185 100 100 0 1961 2080 643 0 61 457 100 100 0 1.346 1.277 1.278 1.271 1.311 1.296 0.681 80 398 4600 4736 0.428 2639 1961 2656 2080 212477 166397 14.103 4.418 -50 0
5 2820 4510 100 48 79 92 0 27 114 23 8 0 28 68 86 0 25 313 1 0 0 1.714 1.162 0.681 0.826 3.679 0.260 0.455 80 406 76 147 0.778 48 28 79 68 6302 5417 0.456 0.137 -50 0
6 3000 4510 100 1304 1333 450 0 20 47 100 100 0 414 427 282 0 8 27 96 93 0 3.150 3.122 3.429 3.645 2.102 3.159 0.559 80 406 1718 1760 1.655 1304 414 1333 427 106656 34197 27.936 15.519 -50 0
7 3180 4510 100 1756 1810 621 0 22 48 100 100 0 935 960 421 0 7 34 100 100 0 1.878 1.885 2.061 1.965 1.530 1.988 0.734 80 406 2691 2770 0.909 1756 935 1810 960 144834 76814 37.250 28.029 -50 0
8 3360 4510 100 0 26 44 0 19 48 21 10 0 0 32 68 0 6 33 23 16 0 0.000 0.813 0.406 0.607 3.985 0.252 0.005 80 438 0 58 NULL 0 0 26 32 2089 2532 0.146 0.788 -50 0
9 3540 4510 100 710 732 289 0 18 43 100 98 0 21 64 89 0 5 19 51 46 0 33.810 11.438 6.947 7.401 2.399 14.636 0.173 80 406 731 796 5.079 710 21 732 64 58556 5154 16.605 3.105 -50 0
10 3720 4510 100 264 280 179 0 19 43 91 88 0 2 46 68 0 8 29 37 31 0 132.000 6.087 3.506 3.974 2.786 8.949 0.110 80 426 266 326 7.044 264 2 280 46 22365 3712 6.070 1.310 -50 0
11 3900 4510 100 581 563 245 0 16 37 98 97 0 437 478 276 0 9 44 95 90 0 1.330 1.178 1.159 1.321 2.046 1.229 0.564 80 389 1018 1041 0.411 581 437 563 478 45046 38214 14.784 10.659 -50 0
12 4080 4520 120 4545 4308 1668 0 17 43 98 98 0 2106 1924 1030 0 8 41 90 90 0 2.158 2.239 2.237 2.495 1.895 2.157 0.854 120 464 6651 6232 1.110 4545 2106 4308 1924 517019 230860 99.791 46.732 0 0
13 4260 4510 100 603 613 298 0 13 39 98 98 0 0 39 74 0 7 25 32 25 0 100000.000 15.718 8.808 8.739 3.245 31.422 0.051 80 385 603 652 16.610 603 0 613 39 49016 3126 15.385 1.280 -50 0
14 4440 4520 100 44 68 87 0 16 54 45 21 0 21 55 72 0 9 27 43 37 0 2.095 1.236 1.000 1.166 3.526 2.023 0.050 80 414 65 123 1.067 44 21 68 55 5442 4381 0.963 1.704 -50 0
15 4620 4520 100 132 157 146 0 17 55 76 52 0 24 49 71 0 7 27 47 27 0 5.500 3.204 1.981 2.100 3.997 6.358 0.050 80 426 156 206 2.459 132 24 157 49 12534 3921 2.545 1.556 -50 0
16 4800 4520 100 211 225 155 0 19 38 90 78 0 51 85 122 0 7 25 55 50 0 4.137 2.647 1.851 2.678 3.929 2.541 0.259 80 426 262 310 2.049 211 51 225 85 17962 6837 5.421 3.120 -50 0
17 4980 4520 100 337 379 186 0 20 38 100 100 0 209 265 248 0 5 20 87 83 0 1.612 1.430 1.411 1.700 2.747 1.183 0.389 80 426 546 644 0.689 337 209 379 265 30318 21220 9.447 13.000 -50 0
18 5160 4520 100 315 319 183 0 16 36 96 96 0 104 128 126 0 7 26 77 66 0 3.029 2.492 2.345 2.273 3.016 3.051 0.200 80 426 419 447 1.599 315 104 319 128 25481 10275 8.417 4.654 -50 0
19 5340 4520 100 53 83 100 0 19 42 53 36 0 38 60 84 0 6 25 55 37 0 1.395 1.383 1.155 1.074 2.599 1.284 0.058 80 426 91 143 0.480 53 38 83 60 6623 4839 1.524 2.160 -50 0
20 5520 4520 100 547 580 273 0 19 42 100 100 0 590 647 308 0 7 30 98 97 0 0.927 0.896 0.859 0.916 1.983 0.888 0.592 80 426 1137 1227 -0.109 547 590 580 647 46434 51749 13.357 21.333 -50 0

Total number of rows: 17664

Table truncated, full table size 3067 Kbytes.




Supplementary data files not provided
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