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Sample GSM49451 Query DataSets for GSM49451
Status Public on Jan 01, 2006
Title Chimp4VSRef42b
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 4 vs Reference slide 42b
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 6700 15420 110 4138 4714 2757 48 50 14 100 100 0 4905 5511 3085 61 64 16 100 100 0 0.844 0.856 0.843 0.828 1.260 0.867 0.985 102 480 8929 10111 -0.245 4087 4842 4663 5448 480864 333.143 0 0
YG-CHIMP-0036 2620 15610 80 746 672 230 83 87 39 100 97 0 747 676 219 104 107 40 100 100 0 1.028 1.027 1.041 1.017 1.308 1.029 0.964 49 261 1290 1145 0.040 654 636 580 565 32916 15.000 0 0
YG-CHIMP-0060 2790 15590 100 765 715 425 96 98 25 100 97 0 817 753 408 117 117 21 100 98 0 0.964 0.982 0.923 0.949 1.310 1.000 0.965 78 343 1353 1239 -0.053 664 689 614 625 55764 24.680 0 0
YG-CHIMP-0084 2940 15600 100 1698 1609 920 109 110 26 100 100 0 1722 1542 841 126 129 24 100 100 0 1.002 1.066 1.075 1.033 1.313 1.074 0.975 74 288 3191 2922 0.003 1597 1594 1508 1414 119076 57.654 0 0
YG-CHIMP-0010 3110 15580 90 962 950 515 87 91 27 100 100 0 1019 997 515 106 110 27 100 100 0 0.966 0.977 0.944 0.957 1.203 0.981 0.975 85 270 1752 1718 -0.049 861 891 849 869 80781 31.815 0 0
YG-CHIMP-0034 3280 15590 90 954 749 495 63 70 25 98 95 0 881 788 481 80 83 23 100 100 0 1.107 0.959 0.945 0.900 1.296 0.991 0.977 74 260 1650 1352 0.147 867 783 662 690 55392 27.160 0 0
YG-CHIMP-0058 3450 15600 80 699 637 250 52 52 11 100 100 0 720 691 241 65 66 11 100 100 0 0.989 0.936 0.942 0.891 1.328 0.950 0.968 55 257 1293 1202 -0.016 643 650 581 621 35039 53.182 0 0
YG-CHIMP-0082 3630 15590 120 414 484 357 50 51 11 100 100 0 509 566 400 63 64 13 100 100 0 0.812 0.859 0.869 0.824 1.418 0.877 0.971 88 449 808 935 -0.301 362 446 432 503 42614 39.364 0 0
YG-CHIMP-0008 3800 15620 60 1304 1097 612 47 49 13 100 100 0 1298 1086 536 62 63 13 100 100 0 1.015 1.023 1.052 0.907 1.668 1.056 0.950 22 145 2491 2072 0.022 1255 1236 1048 1024 24137 80.615 0 0
YG-CHIMP-0032 3980 15590 100 2007 2970 2126 47 51 17 100 100 0 1476 1942 1316 61 63 15 100 100 0 1.384 1.553 1.543 1.507 1.259 1.583 0.986 96 359 3373 4802 0.469 1958 1415 2921 1881 285090 171.706 0 0
YG-CHIMP-0056 4150 15610 90 959 881 387 48 52 19 100 100 0 1101 1029 394 61 65 21 100 100 0 0.876 0.861 0.880 0.822 1.296 0.880 0.963 58 242 1951 1801 -0.191 911 1040 833 968 51085 43.632 0 0
YG-CHIMP-0080 4310 15590 110 533 798 651 48 50 12 100 100 0 693 806 633 59 60 11 100 100 0 0.769 1.008 1.018 0.997 1.295 1.015 0.968 93 330 1116 1494 -0.380 485 631 750 744 74180 62.333 0 0
YG-CHIMP-0006 4480 15590 110 7401 11506 8383 48 50 13 100 100 0 2197 3368 2279 60 60 10 100 100 0 3.444 3.466 3.472 3.370 1.375 3.622 0.955 103 327 9488 14764 1.784 7353 2135 11458 3306 1185107 881.231 0 0
YG-CHIMP-0030 4640 15590 120 254 763 766 48 50 14 100 99 0 295 653 542 61 61 11 100 99 0 0.871 1.205 1.047 1.129 1.592 1.341 0.879 102 396 436 1303 -0.199 203 233 712 591 77855 50.929 0 0
YG-CHIMP-0054 4820 15580 110 1555 2574 1950 50 53 21 100 100 0 1238 1906 1378 61 63 15 100 100 0 1.278 1.368 1.340 1.327 1.305 1.392 0.982 105 341 2679 4366 0.354 1503 1176 2522 1844 270277 120.048 0 0
YG-CHIMP-0078 4990 15590 110 307 750 908 51 53 20 100 100 0 352 736 667 63 64 15 100 100 0 0.879 1.036 0.876 0.950 1.706 1.260 0.816 96 331 545 1372 -0.186 255 290 698 674 72006 34.850 0 0
YG-CHIMP-0004 5170 15590 120 364 655 546 50 51 14 99 98 0 343 666 529 63 64 13 100 99 0 1.110 0.998 0.969 1.039 1.535 1.018 0.949 106 392 593 1207 0.151 312 281 603 604 69468 43.143 0 0
YG-CHIMP-0028 5330 15600 110 469 626 534 49 49 10 100 100 0 413 676 545 61 61 10 100 100 0 1.191 0.936 0.924 0.911 1.446 0.960 0.956 95 328 769 1189 0.252 418 351 575 614 59504 57.700 0 0
YG-CHIMP-0052 5500 15600 80 993 1036 590 49 49 10 100 100 0 1112 1083 578 62 63 10 100 100 0 0.900 0.968 0.977 0.959 1.381 0.984 0.968 59 225 1995 2009 -0.152 945 1050 988 1021 61141 98.700 0 0
YG-CHIMP-0076 5680 15590 100 659 634 412 47 48 10 100 97 0 947 808 511 61 61 10 100 100 0 0.688 0.782 0.788 0.748 1.482 0.788 0.974 80 351 1499 1335 -0.539 611 888 586 749 50716 58.600 0 0

Total number of rows: 4224

Table truncated, full table size 811 Kbytes.




Supplementary data files not provided
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