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Sample GSM48220 Query DataSets for GSM48220
Status Public on Apr 21, 2005
Title C-6-3
Sample type RNA
 
Channel 1
Source name cy3 Pool
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 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 1890 5760 100 490 786 638 363 370 96 52 42 0 808 916 392 396 400 65 95 87 0 0.308 0.813 0.683 0.506 2.645 1.330 0.664 80 414 539 943 -1.698 127 412 423 520 62914 73251 4.333 7.938 0 0
2 2050 5760 90 816 841 203 369 375 95 98 92 0 3448 3453 566 397 410 164 100 100 0 0.147 0.154 0.163 0.147 1.496 0.154 0.696 52 355 3498 3528 -2.771 447 3051 472 3056 43734 179544 4.905 18.555 0 0
3 2240 5760 90 858 858 234 367 369 95 98 86 0 1148 1154 201 384 387 66 100 100 0 0.643 0.638 0.668 0.566 2.007 0.637 0.535 52 373 1255 1261 -0.638 491 764 491 770 44610 60017 5.147 11.621 0 0
4 2420 5770 100 2350 2401 813 364 365 102 100 100 0 2081 2060 419 400 407 76 100 100 0 1.181 1.227 1.255 1.172 1.402 1.301 0.871 80 436 3667 3697 0.241 1986 1681 2037 1660 192073 164765 19.961 21.750 0 0
5 2600 5770 100 457 457 136 345 357 100 55 25 0 974 990 146 408 421 82 100 100 0 0.198 0.192 0.246 0.226 2.185 0.205 0.166 80 426 678 694 -2.337 112 566 112 582 36547 79193 1.000 6.939 0 0
6 2770 5760 90 781 763 193 364 360 94 96 82 0 1653 1686 310 393 407 113 100 100 0 0.331 0.309 0.311 0.275 1.870 0.310 0.733 52 366 1677 1692 -1.595 417 1260 399 1293 39689 87692 4.287 11.319 0 0
7 2960 5770 100 1639 1643 461 353 359 100 100 100 0 2208 2242 533 373 384 108 100 100 0 0.701 0.690 0.687 0.669 1.304 0.696 0.903 80 445 3121 3159 -0.513 1286 1835 1290 1869 131426 179396 12.840 17.204 0 0
8 3140 5770 110 481 488 118 353 359 96 56 31 0 796 795 194 352 355 63 98 97 0 0.288 0.305 0.312 0.286 2.994 0.251 0.134 80 464 572 578 -1.794 128 444 135 443 39047 63631 1.344 6.984 0 0
9 3320 5770 100 502 513 137 349 357 99 68 30 0 1184 1170 208 337 343 61 100 100 0 0.181 0.197 0.196 0.188 2.200 0.170 0.213 80 426 1000 997 -2.469 153 847 164 833 41001 93627 1.576 13.557 0 0
10 3500 5770 110 463 473 127 361 368 101 50 23 0 819 833 152 318 320 56 100 100 0 0.204 0.217 0.268 0.211 3.004 0.233 0.125 80 464 603 627 -2.296 102 501 112 515 37855 66613 1.040 9.161 0 0
11 3680 5770 100 939 961 225 377 386 103 100 96 0 854 857 145 300 303 52 100 100 0 1.014 1.048 1.029 0.998 1.516 1.107 0.684 80 426 1116 1141 0.021 562 554 584 557 76862 68535 5.583 10.654 0 0
12 3860 5770 100 4882 4739 1257 381 392 111 100 100 0 4246 4147 904 293 298 51 100 100 0 1.139 1.131 1.132 1.107 1.204 1.145 0.961 80 426 8454 8212 0.187 4501 3953 4358 3854 379113 331723 39.162 75.471 0 0
13 4040 5770 100 537 549 128 379 390 104 66 35 0 1149 1121 211 297 298 50 100 100 0 0.185 0.206 0.213 0.182 2.310 0.180 0.242 80 426 1010 994 -2.431 158 852 170 824 43892 89669 1.529 16.460 0 0
14 4220 5770 100 531 532 116 381 385 101 62 37 0 631 628 97 292 295 52 100 100 0 0.442 0.449 0.489 0.405 2.268 0.522 0.211 80 426 489 487 -1.176 150 339 151 336 42597 50256 1.455 6.404 0 0
15 4400 5770 100 612 655 174 379 379 101 87 65 0 767 774 120 298 300 52 100 100 0 0.497 0.580 0.560 0.543 1.811 0.690 0.494 80 436 702 752 -1.009 233 469 276 476 52390 61880 2.733 9.115 0 0
16 4580 5760 90 623 620 133 396 400 110 80 50 0 777 781 105 310 313 61 100 100 0 0.486 0.476 0.544 0.468 1.816 0.463 0.292 52 368 694 695 -1.041 227 467 224 471 32254 40587 2.000 7.672 0 0
17 4760 5770 100 533 569 139 386 396 108 65 35 0 853 871 136 310 316 66 100 100 0 0.271 0.326 0.293 0.285 2.150 0.330 0.266 80 436 690 744 -1.885 147 543 183 561 45516 69716 1.602 8.409 0 0
18 4940 5770 100 1046 1055 214 385 393 102 100 100 0 1539 1532 193 314 325 67 100 100 0 0.540 0.550 0.535 0.528 1.398 0.552 0.785 80 426 1886 1888 -0.890 661 1225 670 1218 84374 122591 6.490 18.015 0 0
19 5120 5770 100 509 510 114 384 392 107 58 23 0 672 750 217 310 314 53 100 98 0 0.345 0.286 0.372 0.320 2.388 0.260 0.123 80 426 487 566 -1.534 125 362 126 440 40819 60026 1.103 8.226 0 0
20 5300 5770 100 1616 1551 377 388 395 111 100 100 0 1367 1394 259 317 322 64 100 100 0 1.170 1.080 1.130 1.043 1.531 1.127 0.772 80 446 2278 2240 0.226 1228 1050 1163 1077 124072 111487 10.414 16.750 0 0

Total number of rows: 17664

Table truncated, full table size 3410 Kbytes.




Supplementary data files not provided
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