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Sample GSM48173 Query DataSets for GSM48173
Status Public on Apr 21, 2005
Title C-1-1
Sample type RNA
 
Channel 1
Source name cy3 Liver5
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 2300 5770 100 601 606 313 546 567 241 23 10 0 697 716 262 338 392 214 67 40 0 0.153 0.159 0.602 0.646 3.060 1.071 0.010 80 400 414 438 -2.706 55 359 60 378 48441 57268 0.162 1.514 -50 0
2 2480 5780 100 3905 3863 934 470 505 235 100 98 0 976 1008 305 314 369 215 96 82 0 5.189 4.889 4.998 5.157 1.660 5.562 0.574 80 426 4097 4087 2.375 3435 662 3393 694 309008 80623 14.289 2.972 0 0
3 2660 5780 100 822 919 281 426 451 211 83 47 0 1183 1196 291 292 342 215 100 93 0 0.444 0.545 0.515 0.481 2.010 0.555 0.370 80 414 1287 1397 -1.170 396 891 493 904 73545 95675 2.218 3.972 0 0
4 2840 5780 100 2463 2457 508 388 416 190 100 100 0 3343 3360 744 292 333 191 100 100 0 0.680 0.674 0.699 0.676 1.351 0.661 0.837 80 436 5126 5137 -0.556 2075 3051 2069 3068 196599 268831 10.742 15.848 0 0
5 3020 5770 100 313 356 210 379 404 199 17 3 0 515 578 250 285 327 185 58 28 0 -0.287 -0.078 0.541 0.663 2.644 0.279 0.013 80 416 164 270 NULL -66 230 -23 293 28497 46244 -0.241 1.357 -50 0
6 3200 5780 100 1839 1871 423 369 397 204 100 100 0 1426 1497 408 267 303 171 100 100 0 1.268 1.221 1.274 1.232 1.466 1.257 0.696 80 436 2629 2732 0.343 1470 1159 1502 1230 149716 119799 7.225 6.982 0 0
7 3380 5780 100 2027 2021 446 351 382 194 100 100 0 1695 1717 356 266 300 152 100 100 0 1.173 1.151 1.116 1.140 1.410 1.174 0.789 80 426 3105 3121 0.230 1676 1429 1670 1451 161691 137396 8.448 9.322 0 0
8 3560 5780 100 271 292 149 368 399 200 6 0 0 510 527 140 281 319 175 67 17 0 -0.424 -0.309 0.441 0.331 3.153 0.007 0.000 80 426 132 170 NULL -97 229 -76 246 23376 42140 -0.535 1.189 -50 0
9 3740 5780 100 1008 1074 364 387 408 200 96 81 0 569 617 212 284 320 181 75 35 0 2.179 2.063 2.160 2.254 2.408 3.018 0.216 80 426 906 1020 1.124 621 285 687 333 85921 49355 3.330 1.641 0 0
10 3920 5780 100 452 483 211 381 407 203 28 6 0 565 608 207 276 324 191 76 31 0 0.246 0.307 0.644 0.543 3.424 0.505 0.018 80 426 360 434 -2.025 71 289 102 332 38674 48630 0.374 1.487 -50 0
11 4100 5780 100 1018 1038 317 380 407 199 93 81 0 1295 1357 362 274 326 200 100 98 0 0.625 0.608 0.619 0.558 1.933 0.585 0.477 80 426 1659 1741 -0.678 638 1021 658 1083 83056 108564 3.171 5.155 0 0
12 4280 5780 100 3298 3350 626 371 400 186 100 100 0 3340 3343 729 284 326 187 100 100 0 0.958 0.974 0.974 0.978 1.336 0.975 0.859 80 445 5983 6038 -0.062 2927 3056 2979 3059 267961 267416 15.860 16.134 0 0
13 4460 5780 100 707 724 236 360 401 198 75 40 0 513 526 150 285 328 189 60 18 0 1.522 1.510 1.535 1.510 2.423 1.758 0.085 80 426 575 605 0.606 347 228 364 241 57907 42046 1.631 1.048 -50 0
14 4640 5780 100 305 382 275 354 385 193 17 11 0 516 573 242 277 322 180 68 25 0 -0.205 0.095 0.444 0.415 3.298 0.280 0.073 80 426 190 324 NULL -49 239 28 296 30558 45855 -0.016 1.394 -50 0
15 4820 5780 100 497 509 238 388 445 646 5 0 0 605 636 214 278 453 1968 0 0 0 0.333 0.338 0.611 0.517 2.952 0.933 0.046 80 426 436 479 -1.585 109 327 121 358 40682 50847 0.099 0.093 -50 0
16 5000 5780 100 367 406 221 403 464 647 2 0 0 566 604 215 263 438 1969 0 0 0 -0.119 0.009 0.539 0.412 3.012 0.232 0.001 80 426 267 344 NULL -36 303 3 341 32454 48296 -0.090 0.084 -50 0
17 5180 5790 100 630 655 260 372 399 202 56 28 0 679 712 225 258 309 275 77 25 0 0.613 0.623 0.717 0.654 2.314 1.030 0.124 80 449 679 737 -0.706 258 421 283 454 52407 56936 1.267 1.465 0 0
18 5370 5780 90 600 647 277 381 419 245 48 23 0 670 706 290 264 321 336 61 13 0 0.539 0.602 0.668 0.670 2.492 0.847 0.388 52 378 625 708 -0.891 219 406 266 442 33659 36693 0.931 1.146 0 0
19 5540 5780 100 317 344 170 368 401 226 7 2 0 534 541 167 265 315 257 52 6 0 -0.190 -0.087 0.341 0.357 3.000 0.804 0.183 80 426 218 252 NULL -51 269 -24 276 27547 43267 -0.252 0.879 -50 0
20 5720 5790 100 819 829 242 372 396 188 83 62 0 1248 1404 817 261 299 179 100 100 0 0.453 0.400 0.425 0.393 1.902 0.280 0.315 80 430 1434 1600 -1.143 447 987 457 1143 66291 112288 2.303 6.173 0 0

Total number of rows: 17664

Table truncated, full table size 3394 Kbytes.




Supplementary data files not provided
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