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Sample GSM48228 Query DataSets for GSM48228
Status Public on Apr 21, 2005
Title C-7-3
Sample type RNA
 
Channel 1
Source name cy3 Pool
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 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 2020 4310 100 1 57 91 0 6 17 43 40 0 0 21 38 0 7 28 23 15 0 100000.000 2.714 2.120 1.816 8.877 9.338 0.016 80 369 1 78 16.610 1 0 57 21 4528 1666 3.000 0.500 -50 0
2 2190 4320 120 828 792 490 0 9 31 90 90 0 3699 3236 1648 0 10 40 92 91 0 0.224 0.245 0.233 0.219 2.264 0.231 0.775 120 453 4527 4028 -2.159 828 3699 792 3236 95028 388351 25.258 80.650 0 0
3 2370 4320 110 819 810 322 0 12 40 98 98 0 772 821 400 0 27 232 96 85 0 1.061 0.987 1.009 0.976 2.053 0.929 0.632 80 407 1591 1631 0.085 819 772 810 821 64821 65663 19.950 3.422 0 0
4 2550 4310 120 2696 2513 965 0 173 3116 25 0 0 2109 1935 1001 0 24 222 88 84 0 1.278 1.299 1.274 1.449 2.094 9.651 0.090 120 445 4805 4448 0.354 2696 2109 2513 1935 301520 232234 0.751 8.608 0 0
5 2730 4320 100 41 66 102 0 5 17 60 53 0 41 93 148 0 8 28 55 47 0 1.000 0.710 0.656 0.772 4.299 0.100 0.015 80 392 82 159 0.000 41 41 66 93 5244 7446 3.588 3.036 0 0
6 2910 4320 110 663 646 222 0 6 27 100 100 0 1123 1177 384 0 7 25 100 100 0 0.590 0.549 0.561 0.551 1.574 0.510 0.783 80 431 1786 1823 -0.760 663 1123 646 1177 51664 94144 23.704 46.800 0 0
7 3090 4320 120 1313 1219 641 0 6 28 95 92 0 1789 1634 885 0 6 23 93 92 0 0.734 0.746 0.747 0.778 2.117 0.712 0.817 120 480 3102 2853 -0.446 1313 1789 1219 1634 146249 196023 43.321 70.783 0 0
8 3280 4320 100 0 31 75 0 6 33 22 12 0 0 35 61 0 7 34 32 23 0 0.000 0.886 0.963 0.732 5.382 4.218 0.037 80 410 0 66 NULL 0 0 31 35 2444 2787 0.758 0.824 -50 0
9 3450 4320 100 13 59 98 0 7 35 42 31 0 587 626 288 0 7 34 100 100 0 0.022 0.094 0.129 0.123 2.874 0.057 0.108 80 407 600 685 -5.497 13 587 59 626 4708 50051 1.486 18.206 0 0
10 3640 4320 100 27 91 165 0 7 23 52 47 0 193 200 146 0 7 26 88 83 0 0.140 0.455 0.335 0.332 3.359 0.424 0.144 80 428 220 291 -2.838 27 193 91 200 7261 15974 3.652 7.423 -50 0
11 3820 4320 120 409 403 239 0 6 21 90 88 0 427 398 253 0 7 22 90 90 0 0.958 1.013 1.009 1.105 2.358 1.047 0.498 120 446 836 801 -0.062 409 427 403 398 48401 47713 18.905 17.773 0 0
12 3990 4320 120 2523 2196 1030 0 5 22 95 95 0 3391 3076 1498 0 16 169 90 90 0 0.744 0.714 0.736 0.709 2.035 0.684 0.862 120 461 5914 5272 -0.427 2523 3391 2196 3076 263539 369115 99.591 18.107 0 0
13 4180 4320 100 1 27 40 0 4 19 38 26 0 533 549 219 0 11 61 98 98 0 0.002 0.049 0.086 0.087 2.320 0.023 0.054 80 422 534 576 -9.058 1 533 27 549 2160 43938 1.211 8.820 0 0
14 4360 4320 110 2 89 354 0 4 17 46 33 0 11 53 80 0 11 60 28 17 0 0.182 1.679 0.673 0.773 5.469 18.124 0.032 80 450 13 142 -2.459 2 11 89 53 7090 4211 5.000 0.700 0 0
15 4530 4320 110 88 109 120 0 5 33 70 58 0 74 90 93 0 5 21 70 60 0 1.189 1.211 1.124 1.096 4.187 1.676 0.087 80 462 162 199 0.250 88 74 109 90 8741 7200 3.152 4.048 0 0
16 4720 4320 110 86 144 250 0 4 22 68 63 0 141 163 125 0 7 26 88 78 0 0.610 0.883 0.723 0.762 3.589 1.814 0.190 80 476 227 307 -0.713 86 141 144 163 11531 13050 6.364 6.000 0 0
17 4900 4320 110 179 211 141 0 18 215 41 7 0 331 368 234 0 6 25 95 93 0 0.541 0.573 0.600 0.577 2.966 3.125 0.060 80 472 510 579 -0.887 179 331 211 368 16844 29409 0.898 14.480 0 0
18 5070 4320 110 96 133 109 0 7 52 75 48 0 351 365 212 0 6 23 97 97 0 0.274 0.364 0.384 0.335 2.904 0.218 0.264 80 450 447 498 -1.870 96 351 133 365 10629 29211 2.423 15.609 0 0
19 5250 4320 110 9 43 69 0 5 21 37 30 0 22 63 86 0 6 24 48 37 0 0.409 0.683 0.776 0.741 4.283 0.019 0.004 80 457 31 106 -1.290 9 22 43 63 3405 5023 1.810 2.375 0 0
20 5440 4330 110 554 570 262 0 4 19 98 97 0 432 472 238 0 5 21 100 100 0 1.282 1.208 1.154 1.198 2.014 1.251 0.547 80 462 986 1042 0.359 554 432 570 472 45603 37742 29.789 22.238 0 0

Total number of rows: 17664

Table truncated, full table size 2957 Kbytes.




Supplementary data files not provided
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