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Sample GSM48402 Query DataSets for GSM48402
Status Public on Apr 21, 2005
Title R-1-cDNA-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 18, 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 GPL1967
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 the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 1 (635 nm).
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 1 (635 nm).
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 standard deviation of the feature intensity at wavelength 2 (532 nm).
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 the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 2 (532 nm).
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength 2 that are saturated.
F3 Median genepix output.
F3 Mean genepix output.
F3 SD genepix output.
B3 Median genepix output.
B3 Mean genepix output.
B3 SD genepix output.
% > B3+1SD genepix output.
% > B3+2SD genepix output.
F3 % Sat.
F4 Median genepix output.
F4 Mean genepix output.
F4 SD genepix output.
B4 Median genepix output.
B4 Mean genepix output.
B4 SD genepix output.
% > B4+1SD genepix output.
% > B4+2SD genepix output.
F4 % Sat. genepix output.
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.
Ratio of Medians (Ratio/2) genepix output.
Ratio of Means (Ratio/2) genepix output.
Median of Ratios (Ratio/2) genepix output.
Mean of Ratios (Ratio/2) genepix output.
Ratios SD (Ratio/2) genepix output.
Rgn Ratio (Ratio/2) genepix output.
Rgn R² (Ratio/2)
Ratio of Medians (Ratio/3) genepix output.
Ratio of Means (Ratio/3) genepix output.
Median of Ratios (Ratio/3) genepix output.
Mean of Ratios (Ratio/3) genepix output.
Ratios SD (Ratio/3) genepix output.
Rgn Ratio (Ratio/3) genepix output.
Rgn R² (Ratio/3)
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.
Log Ratio (Ratio/2) genepix output.
Log Ratio (Ratio/3) genepix output.
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.
F3 Median - B3 genepix output.
F4 Median - B4 genepix output.
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.
F3 Mean - B3 genepix output.
F4 Mean - B4 genepix output.
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. F3 Median F3 Mean F3 SD B3 Median B3 Mean B3 SD % > B3+1SD % > B3+2SD F3 % Sat. F4 Median F4 Mean F4 SD B4 Median B4 Mean B4 SD % > B4+1SD % > B4+2SD F4 % 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) Ratio of Medians (Ratio/2) Ratio of Means (Ratio/2) Median of Ratios (Ratio/2) Mean of Ratios (Ratio/2) Ratios SD (Ratio/2) Rgn Ratio (Ratio/2) Rgn R² (Ratio/2) Ratio of Medians (Ratio/3) Ratio of Means (Ratio/3) Median of Ratios (Ratio/3) Mean of Ratios (Ratio/3) Ratios SD (Ratio/3) Rgn Ratio (Ratio/3) Rgn R² (Ratio/3) F Pixels B Pixels Sum of Medians Sum of Means VALUE Log Ratio (Ratio/2) Log Ratio (Ratio/3) F635 Median - B635 F532 Median - B532 F3 Median - B3 F4 Median - B4 F635 Mean - B635 F532 Mean - B532 F3 Mean - B3 F4 Mean - B4 Flags Normalize
1 2600 2410 110 3854 4060 1776 186 222 164 100 100 0 4509 4486 1771 285 318 189 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.868 0.922 0.941 0.905 1.307 0.933 0.909 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 605 7892 8075 -0.204 NULL NULL 3668 4224 0 0 3874 4201 0 0 0 0
2 2790 2400 70 348 379 134 209 244 167 46 9 0 447 499 267 279 309 174 50 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.827 0.773 0.942 0.719 4.870 0.125 0.009 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 32 220 307 390 -0.273 NULL NULL 139 168 0 0 170 220 0 0 0 0
3 2960 2410 100 231 237 130 201 255 200 12 0 0 281 335 223 283 332 313 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -15.000 0.692 1.036 1.064 4.599 58.930 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 506 28 88 NULL NULL NULL 30 -2 0 0 36 52 0 0 -50 0
4 3160 2410 110 2166 2246 923 193 238 179 100 98 0 2220 2282 1007 272 329 244 98 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.013 1.021 1.015 1.055 1.519 0.985 0.777 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 511 3921 4063 0.018 NULL NULL 1973 1948 0 0 2053 2010 0 0 0 0
5 3320 2410 100 190 230 183 199 235 166 16 6 0 281 330 175 271 321 229 11 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -0.900 0.525 1.161 1.094 4.982 0.274 0.016 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 454 1 90 NULL NULL NULL -9 10 0 0 31 59 0 0 -50 0
6 3510 2420 120 2234 2144 1097 205 248 183 96 90 0 2751 2740 1532 277 319 200 94 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.820 0.787 0.811 0.834 2.015 0.733 0.768 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 120 596 4503 4402 -0.286 NULL NULL 2029 2474 0 0 1939 2463 0 0 0 0
7 3680 2410 100 220 277 202 214 265 198 16 7 0 334 361 196 286 332 281 12 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.125 0.840 1.129 1.270 5.493 0.415 0.005 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 444 54 138 -3.000 NULL NULL 6 48 0 0 63 75 0 0 -50 0
8 3880 2420 100 436 491 257 213 262 200 53 28 0 447 533 287 270 338 345 35 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.260 1.057 0.842 1.184 4.169 0.198 0.025 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 493 400 541 0.333 NULL NULL 223 177 0 0 278 263 0 0 0 0
9 4050 2410 90 411 429 222 210 263 211 44 17 0 458 544 345 285 338 316 32 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.162 0.846 0.819 0.790 4.056 0.914 0.014 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 52 355 374 478 0.216 NULL NULL 201 173 0 0 219 259 0 0 0 0
10 4220 2420 100 926 919 388 210 272 224 91 70 0 807 895 430 282 379 819 27 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.364 1.157 1.170 1.207 2.600 1.003 0.203 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 474 1241 1322 0.448 NULL NULL 716 525 0 0 709 613 0 0 0 0
11 4410 2420 100 233 325 326 214 269 222 20 10 0 363 388 171 290 400 851 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.260 1.133 1.254 1.177 4.362 0.134 0.205 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 442 92 209 -1.942 NULL NULL 19 73 0 0 111 98 0 0 -50 0
12 4580 2420 120 612 637 266 230 279 209 78 44 0 749 792 432 289 356 282 65 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.830 0.809 0.781 0.833 3.195 0.473 0.149 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 120 592 842 910 -0.268 NULL NULL 382 460 0 0 407 503 0 0 0 0
13 4770 2420 100 224 251 168 232 282 203 11 2 0 283 352 235 282 326 211 10 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -8.000 0.271 1.400 1.239 3.858 2.272 0.007 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 452 -7 89 NULL NULL NULL -8 1 0 0 19 70 0 0 -50 0
14 4950 2420 100 236 306 222 232 280 201 25 8 0 313 355 190 293 319 150 25 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.200 1.194 1.259 1.070 4.466 0.047 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 439 24 136 -2.322 NULL NULL 4 20 0 0 74 62 0 0 -50 0
15 5130 2430 130 3668 4398 3011 228 282 203 99 98 0 4130 4816 3308 291 328 190 99 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.896 0.922 0.926 0.938 1.464 0.912 0.926 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 120 694 7279 8695 -0.158 NULL NULL 3440 3839 0 0 4170 4525 0 0 0 0
16 5310 2420 100 1095 1112 412 229 277 194 95 87 0 1305 1362 472 293 324 165 98 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.856 0.826 0.770 0.777 2.359 0.777 0.427 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 449 1878 1952 -0.225 NULL NULL 866 1012 0 0 883 1069 0 0 0 0
17 5490 2420 80 638 712 365 220 268 195 80 55 0 635 803 444 296 338 207 75 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.233 0.970 1.271 1.102 3.144 0.802 0.193 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 52 314 757 999 0.302 NULL NULL 418 339 0 0 492 507 0 0 0 0
18 5670 2420 100 298 337 200 217 272 196 32 11 0 401 441 194 294 347 280 18 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.757 0.816 0.954 1.038 5.067 0.307 0.011 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 482 188 267 -0.402 NULL NULL 81 107 0 0 120 147 0 0 -50 0
19 5830 2400 50 302 424 343 254 313 249 33 16 0 615 797 455 342 415 273 50 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.176 0.374 0.843 0.875 7.595 6.092 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12 80 321 625 -2.508 NULL NULL 48 273 0 0 170 455 0 0 0 0
20 6030 2420 100 278 319 187 231 293 225 22 3 0 340 442 403 303 356 261 21 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.270 0.633 0.786 0.775 4.710 100.340 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 80 508 84 227 0.345 NULL NULL 47 37 0 0 88 139 0 0 -50 0

Total number of rows: 27648

Table truncated, full table size 8273 Kbytes.




Supplementary data files not provided
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