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Sample GSM48178 Query DataSets for GSM48178
Status Public on Apr 21, 2005
Title C-1-7
Sample type RNA
 
Channel 1
Source name cy3 Liver5
Organism Mus musculus
Extracted molecule total RNA
 
Channel 2
Source name cy5 Liver3
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 2000 6400 100 332 356 169 278 293 156 28 12 0 267 267 92 205 212 88 40 10 0 0.871 1.258 1.485 1.911 3.922 15.677 0.005 80 400 116 140 -0.199 54 62 78 62 28443 21378 0.404 0.625 -50 0
2 2180 6400 100 416 451 190 267 292 150 50 25 0 291 291 112 210 220 89 46 17 0 1.840 2.272 2.042 1.661 3.647 18.664 0.004 80 416 230 265 0.879 149 81 184 81 36071 23275 1.060 0.798 -50 0
3 2360 6400 80 506 504 198 278 289 150 63 34 0 334 326 126 216 225 90 57 32 0 1.932 2.055 1.059 1.182 4.212 127.726 0.000 52 314 346 336 0.950 228 118 226 110 26189 16957 1.433 1.122 0 0
4 2540 6410 100 989 1029 388 273 298 161 97 86 0 586 558 173 201 216 83 90 85 0 1.860 2.118 2.375 2.239 2.673 3.650 0.248 80 424 1101 1113 0.895 716 385 756 357 82321 44667 4.540 4.120 0 0
5 2720 6400 100 303 335 165 269 304 170 30 7 0 252 249 89 210 221 83 30 8 0 0.810 1.692 1.224 1.247 3.976 22.022 0.003 80 426 76 105 -0.305 34 42 66 39 26793 19954 0.182 0.337 -50 0
6 2900 6410 80 500 577 234 289 312 173 63 38 0 355 364 103 215 216 81 82 42 0 1.507 1.933 1.749 1.891 3.085 7.305 0.035 52 320 351 437 0.592 211 140 288 149 30002 18922 1.532 1.827 0 0
7 3080 6410 90 617 631 231 279 302 163 80 53 0 364 376 107 216 225 94 75 32 0 2.284 2.200 2.286 2.030 3.348 6.396 0.064 52 371 486 512 1.191 338 148 352 160 32803 19573 2.018 1.606 0 0
8 3260 6400 100 282 293 160 279 298 157 17 5 0 259 272 104 208 213 84 40 12 0 0.059 0.219 1.568 1.472 3.610 13.613 0.009 80 416 54 78 -4.087 3 51 14 64 23420 21731 -0.032 0.702 -50 0
9 3440 6400 100 328 341 150 272 296 157 25 5 0 246 260 95 202 210 84 41 15 0 1.273 1.190 1.704 1.451 4.978 0.061 0.007 80 416 100 127 0.348 56 44 69 58 27264 20814 0.287 0.595 -50 0
10 3620 6400 100 343 344 172 266 296 160 27 10 0 251 248 99 203 212 85 28 7 0 1.604 1.733 1.861 1.649 3.131 91.313 0.000 80 424 125 123 0.682 77 48 78 45 27491 19824 0.300 0.424 -50 0
11 3810 6400 90 571 575 228 278 298 150 71 50 0 306 302 115 202 217 85 51 26 0 2.817 2.970 2.493 2.823 3.355 7.387 0.054 52 366 397 397 1.494 293 104 297 100 29886 15703 1.847 1.000 0 0
12 3980 6410 110 863 879 321 292 315 175 92 75 0 394 399 153 206 214 79 77 60 0 3.037 3.041 2.916 2.915 2.615 4.910 0.175 80 464 759 780 1.603 571 188 587 193 70349 31906 3.223 2.342 0 0
13 4160 6410 100 327 358 182 303 323 175 25 5 0 243 241 91 205 215 84 30 5 0 0.632 1.528 2.328 2.323 3.081 10.658 0.019 80 426 62 91 -0.663 24 38 55 36 28606 19241 0.200 0.310 -50 0
14 4340 6410 100 330 330 164 276 298 159 18 8 0 226 229 77 205 211 81 22 5 0 2.571 2.250 1.587 1.790 3.860 101.142 0.000 80 426 75 78 1.363 54 21 54 24 26427 18356 0.201 0.222 -50 0
15 4520 6410 100 321 336 168 288 305 152 17 7 0 226 230 87 203 212 84 21 6 0 1.435 1.778 2.292 2.394 4.554 84.673 0.000 80 426 56 75 0.521 33 23 48 27 26863 18377 0.204 0.214 -50 0
16 4700 6410 100 330 358 190 301 310 154 25 8 0 240 250 87 215 216 85 20 8 0 1.160 1.629 2.000 1.784 5.768 0.097 0.016 80 426 54 92 0.214 29 25 57 35 28659 19993 0.312 0.400 -50 0
17 4880 6410 100 407 445 240 289 306 155 38 20 0 246 255 85 207 210 80 30 8 0 3.026 3.250 2.547 2.963 4.221 47.518 0.001 80 426 157 204 1.597 118 39 156 48 35603 20402 0.897 0.563 -50 0
18 5060 6410 100 309 360 225 294 307 153 28 15 0 241 240 93 205 212 77 28 13 0 0.417 1.886 1.541 1.760 3.988 13.660 0.013 80 426 51 101 -1.263 15 36 66 35 28788 19172 0.346 0.364 -50 0
19 5240 6410 100 291 313 154 275 297 153 22 5 0 222 234 84 207 215 79 22 8 0 1.067 1.407 1.923 1.592 4.752 28.685 0.003 80 422 31 65 0.093 16 15 38 27 25022 18686 0.105 0.241 -50 0
20 5420 6410 100 492 493 209 296 317 170 56 28 0 268 286 108 211 218 86 40 20 0 3.439 2.627 2.388 2.245 3.737 15.164 0.009 80 426 253 272 1.782 196 57 197 75 39479 22854 1.035 0.791 -50 0

Total number of rows: 17664

Table truncated, full table size 3345 Kbytes.




Supplementary data files not provided

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