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Sample GSM49440 Query DataSets for GSM49440
Status Public on Jan 01, 2006
Title Chimp1VSRef25b
Sample type RNA
 
Channel 1
Source name polyA RNA
Organisms Pan troglodytes; Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name total RNA
Organisms Pan troglodytes; Homo sapiens
Extracted molecule total RNA
 
 
Description data_processing: log base 2 ratio of cy5 to cy3
label_ch1: CY3
characteristics_ch1: human
label_ch2: CY5
Chimpanzee 1 vs Reference slide 25b
characteristics_ch2: Chimp
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 6510 15510 100 2834 3140 1739 53 55 14 100 100 0 7995 8509 4189 69 69 15 100 100 0 0.350 0.365 0.364 0.347 1.318 0.373 0.958 104 391 10704 11524 -1.513 2777 7927 3083 8441 326519 220.357 0 0
YG-CHIMP-0036 2430 15650 100 282 609 583 49 53 18 100 100 0 409 764 616 63 64 18 100 100 0 0.668 0.796 0.775 0.747 1.424 0.882 0.924 110 307 577 1259 -0.583 231 346 558 701 66991 30.889 0 0
YG-CHIMP-0060 2590 15660 100 462 902 713 48 51 15 100 100 0 673 1115 800 61 63 13 100 100 0 0.674 0.809 0.799 0.772 1.295 0.847 0.949 98 324 1021 1903 -0.570 411 610 851 1052 88423 56.733 0 0
YG-CHIMP-0084 2770 15640 100 927 1844 1546 49 52 16 100 100 0 1766 2343 1303 61 64 16 100 100 0 0.514 0.786 0.557 0.618 1.541 0.943 0.921 115 274 2579 4073 -0.959 876 1703 1793 2280 212027 112.000 0 0
YG-CHIMP-0010 2930 15670 100 649 1359 1171 48 50 15 100 100 0 1116 1597 1097 64 64 16 100 100 0 0.569 0.854 0.752 0.720 1.474 0.953 0.928 101 260 1649 2840 -0.814 598 1051 1308 1532 137223 87.267 0 0
YG-CHIMP-0034 3100 15670 110 321 808 793 48 50 14 100 100 0 684 1278 1005 61 61 12 100 100 0 0.431 0.622 0.508 0.502 1.427 0.706 0.965 103 317 886 1967 -1.213 267 619 754 1213 83195 54.143 0 0
YG-CHIMP-0058 3290 15660 110 340 789 668 51 52 14 100 100 0 440 832 611 62 62 13 100 100 0 0.763 0.958 0.910 0.866 1.312 1.028 0.958 99 310 661 1502 -0.391 286 375 735 767 78147 52.643 0 0
YG-CHIMP-0082 3450 15670 120 374 777 684 51 53 17 100 100 0 536 898 665 62 64 26 100 100 0 0.679 0.868 0.808 0.772 1.397 0.948 0.949 109 401 791 1556 -0.558 320 471 723 833 84674 42.588 0 0
YG-CHIMP-0008 3630 15670 50 1231 2617 2971 52 54 16 100 100 0 1613 1800 1316 66 66 14 100 100 0 0.756 1.474 0.979 1.077 1.760 1.964 0.840 27 65 2717 4290 -0.403 1170 1547 2556 1734 70665 160.188 -50 0
YG-CHIMP-0032 3780 15670 100 1913 2728 1517 50 53 15 100 100 0 1397 1945 1000 65 65 13 100 100 0 1.396 1.422 1.429 1.391 1.210 1.462 0.980 97 291 3179 4542 0.481 1852 1327 2667 1875 264644 178.333 0 0
YG-CHIMP-0056 3960 15660 110 371 1019 1106 55 56 16 100 100 0 626 1146 975 69 70 14 100 100 0 0.558 0.890 0.722 0.696 1.480 1.037 0.930 122 328 866 2034 -0.843 310 556 958 1076 124305 60.188 0 0
YG-CHIMP-0080 4140 15650 110 387 793 668 53 60 63 99 93 0 641 1065 748 69 71 30 100 100 0 0.580 0.741 0.656 0.636 1.421 0.813 0.960 116 284 902 1732 -0.787 331 571 737 995 92008 11.635 0 0
YG-CHIMP-0006 4300 15670 100 12664 14588 9965 56 57 16 100 100 0 9075 9329 5336 70 71 14 100 100 0 1.400 1.569 1.478 1.460 1.322 1.690 0.961 97 271 21610 23788 0.485 12604 9006 14528 9260 1415079 908.188 0 0
YG-CHIMP-0030 4460 15670 100 775 1040 675 56 58 16 100 100 0 845 1048 654 71 71 14 100 100 0 0.920 1.000 1.077 0.997 1.405 1.019 0.945 100 284 1492 1960 -0.120 715 777 980 980 103951 61.375 0 0
YG-CHIMP-0054 4640 15660 100 963 1389 790 53 55 14 100 100 0 2318 2876 1219 68 69 14 100 100 0 0.401 0.473 0.448 0.437 1.261 0.514 0.956 110 264 3153 4137 -1.317 903 2250 1329 2808 152799 95.286 0 0
YG-CHIMP-0078 4800 15680 100 1293 1497 907 54 55 13 100 100 0 890 1026 606 68 70 14 100 100 0 1.509 1.508 1.574 1.530 1.290 1.520 0.952 89 287 2055 2395 0.594 1236 819 1440 955 133208 110.923 0 0
YG-CHIMP-0004 4980 15670 100 591 1074 821 55 56 14 100 100 0 734 1219 888 68 70 15 100 100 0 0.801 0.883 0.874 0.860 1.328 0.902 0.966 95 316 1194 2162 -0.320 531 663 1014 1148 101999 72.714 0 0
YG-CHIMP-0028 5150 15670 110 464 1009 928 56 59 15 100 100 0 844 1327 1029 75 77 19 100 100 0 0.523 0.756 0.693 0.673 1.357 0.830 0.954 100 332 1177 2205 -0.936 404 773 949 1256 100911 63.333 0 0
YG-CHIMP-0052 5330 15670 100 708 1337 1278 57 60 25 100 100 0 979 1386 1174 75 79 43 100 100 0 0.712 0.970 0.926 0.867 1.396 1.039 0.960 84 291 1558 2594 -0.490 648 910 1277 1317 112277 51.080 0 0
YG-CHIMP-0076 5480 15690 100 698 1064 727 55 57 15 100 100 0 979 1340 867 69 71 15 100 100 0 0.705 0.793 0.780 0.772 1.234 0.812 0.968 92 284 1552 2279 -0.503 642 910 1008 1271 97897 67.133 0 0

Total number of rows: 4224

Table truncated, full table size 829 Kbytes.




Supplementary data files not provided
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