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Sample GSM49457 Query DataSets for GSM49457
Status Public on Jan 01, 2006
Title Orangutan1VSRef24b
Sample type RNA
 
Channel 1
Source name polyA RNA
Organisms Pongo pygmaeus; Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name total RNA
Organisms Pongo pygmaeus; Homo sapiens
Extracted molecule total RNA
 
 
Description data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human 6
label_ch2: CY5
Orangutan 1 vs Reference slide 24b
characteristics_ch2: orangutan
source_name_ch2: EXP
source_name_ch1: REF
 
Submission date Apr 25, 2005
Last update date Oct 18, 2005
Contact name Yoav Gilad
E-mail(s) yoav.gilad@yale.edu
Phone 203-785-6259
Organization name Yale
Department Genetics
Lab Kevin White
Street address 333 Cedar St.
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL1714
Series (1)
GSE2569 Primate Comparison Study

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 the standard deviation of the feature background intensity at wavelength #1 (635 nm).
% > 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. the percentage of feature pixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the 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.
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 (635/532) the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) 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 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)
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 (635/532) Sum of Means (635/532) VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity SNR 635 Flags Normalize
YG-CHIMP-0012 6360 15660 100 571 762 453 199 203 48 97 93 0 6750 7882 4258 47 47 7 100 100 0 0.056 0.072 0.056 0.058 1.764 0.073 0.757 95 442 7080 8403 -4.152 377 6703 568 7835 72362 11.646 0 0
YG-CHIMP-0036 2290 15850 90 1215 1224 454 278 280 55 100 100 0 989 946 422 48 53 24 98 98 0 1.013 1.071 1.024 1.110 1.997 1.066 0.937 55 246 1896 1862 0.018 954 942 963 899 67324 17.164 0 0
YG-CHIMP-0060 2440 15820 100 621 855 517 267 269 46 100 94 0 590 914 654 46 47 11 100 100 0 0.662 0.684 0.646 0.587 1.489 0.723 0.942 93 385 904 1462 -0.596 360 544 594 868 79513 12.739 0 0
YG-CHIMP-0084 2620 15820 100 1655 1737 719 251 253 44 100 100 0 2209 2237 797 47 47 7 100 100 0 0.649 0.678 0.666 0.641 1.281 0.712 0.955 91 318 3567 3677 -0.623 1404 2163 1486 2191 158098 33.727 0 0
YG-CHIMP-0010 2790 15830 100 544 894 611 247 248 42 99 95 0 812 1145 696 46 46 7 100 100 0 0.387 0.588 0.456 0.429 1.787 0.711 0.921 101 302 1061 1744 -1.370 296 765 646 1098 90310 15.381 0 0
YG-CHIMP-0034 2960 15830 100 1109 1293 851 252 253 43 100 98 0 754 1165 808 46 47 7 100 100 0 1.211 0.930 0.905 0.807 1.426 0.980 0.972 91 303 1563 2158 0.276 856 707 1040 1118 117699 24.186 0 0
YG-CHIMP-0058 3110 15840 90 1183 1229 549 256 257 41 100 100 0 898 839 388 47 49 14 100 100 0 1.093 1.232 1.189 1.149 1.376 1.289 0.963 56 289 1781 1768 0.128 930 851 976 792 68851 23.707 0 0
YG-CHIMP-0082 3310 15820 100 990 1066 580 249 248 41 100 98 0 886 842 495 46 48 13 100 100 0 0.878 1.023 0.999 0.926 1.396 1.085 0.957 66 420 1576 1608 -0.187 737 839 813 795 70331 19.951 0 0
YG-CHIMP-0008 3480 15840 50 1282 1257 625 244 244 45 100 100 0 1240 1078 567 48 49 7 100 100 0 0.870 0.983 1.019 0.916 1.437 1.015 0.949 19 81 2229 2042 -0.201 1037 1192 1012 1030 23889 22.511 -50 0
YG-CHIMP-0032 3650 15830 100 1002 1603 983 255 250 43 100 100 0 1933 2454 1356 49 49 8 100 100 0 0.408 0.569 0.505 0.493 1.316 0.617 0.963 92 321 2654 3776 -1.294 769 1885 1370 2406 147501 31.465 0 0
YG-CHIMP-0056 3810 15830 100 607 1003 770 250 251 42 98 95 0 603 919 745 48 48 7 100 100 0 0.674 0.884 0.775 0.721 1.511 0.956 0.955 88 327 929 1641 -0.569 374 555 770 871 88251 17.905 0 0
YG-CHIMP-0080 3990 15820 90 621 1103 810 246 247 39 100 100 0 552 995 769 50 49 7 100 100 0 0.780 0.924 0.820 0.747 1.409 0.985 0.971 83 244 897 1822 -0.359 393 504 875 947 91520 21.949 0 0
YG-CHIMP-0006 4150 15830 100 8560 10295 7259 236 237 43 100 100 0 6253 7031 4049 50 51 9 100 100 0 1.342 1.441 1.360 1.307 1.354 1.580 0.960 95 360 14533 17046 0.425 8328 6205 10063 6983 978070 233.907 0 0
YG-CHIMP-0030 4330 15810 80 1184 1157 395 229 229 41 100 100 0 843 831 283 49 50 15 100 100 0 1.196 1.180 1.194 1.137 1.277 1.237 0.952 57 258 1748 1709 0.258 952 796 925 784 65965 22.634 0 0
YG-CHIMP-0054 4500 15820 100 712 920 544 228 229 36 100 98 0 1845 2326 1062 48 48 8 100 100 0 0.267 0.302 0.244 0.241 1.582 0.349 0.901 99 333 2278 2967 -1.905 480 1798 688 2279 91046 19.194 0 0
YG-CHIMP-0078 4660 15820 80 788 890 424 217 221 33 100 100 0 691 709 345 47 48 7 100 100 0 0.886 1.017 0.962 0.952 1.285 1.089 0.940 67 237 1209 1329 -0.174 568 641 670 659 59597 20.273 0 0
YG-CHIMP-0004 4830 15820 100 1028 1172 657 217 221 37 100 100 0 872 949 541 48 48 7 100 100 0 0.987 1.062 1.005 0.981 1.300 1.116 0.966 85 374 1633 1854 -0.019 811 822 955 899 99656 25.703 0 0
YG-CHIMP-0028 5010 15820 90 744 900 588 223 225 34 100 100 0 666 851 571 48 49 7 100 100 0 0.856 0.853 0.744 0.698 1.494 0.930 0.949 83 261 1143 1484 -0.225 527 616 683 801 74731 19.853 0 0
YG-CHIMP-0052 5170 15810 90 987 1101 713 218 220 36 100 100 0 884 967 697 50 50 7 100 100 0 0.923 0.964 0.981 0.921 1.317 0.988 0.962 79 257 1604 1801 -0.115 770 834 884 917 86958 24.472 0 0
YG-CHIMP-0076 5340 15820 100 635 724 402 204 207 32 98 95 0 697 739 466 49 49 7 100 100 0 0.665 0.754 0.709 0.670 1.484 0.789 0.940 91 345 1079 1210 -0.588 431 648 520 690 65853 16.156 0 0

Total number of rows: 4224

Table truncated, full table size 821 Kbytes.




Supplementary data files not provided
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