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Sample GSM11013 Query DataSets for GSM11013
Status Public on Nov 15, 2003
Title FE5_CA3_top
Sample type RNA
 
Channel 1
Source name Porcine liver, 5 weeks, male, Yorkshire x Landrace, fed
Organism Sus scrofa
Extracted molecule total RNA
 
Channel 2
Source name Porcine liver, 5 weeks, male, Yorkshire x Landrace, Clofibric Acid (0.5% w/w) treatment for 1 week
Organism Sus scrofa
Extracted molecule total RNA
 
 
Description FE5_CA3_top
 
Submission date Oct 04, 2003
Last update date May 28, 2005
Contact name Yewon Cheon
E-mail(s) yecheon@uiuc.edu
Phone 217-333-7371
Organization name University of Illinois at Urbana Champaign
Street address
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
 
Platform ID GPL518
Series (1)
GSE714 Porcine liver

Data table header descriptions
ID_REF
Block
Column
Row
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Dia. diameter in µm of the feature-indicator
F635 Median median pixel intensity of feature for Cy5 channel
F635 Mean mean pixel intensity of feature for Cy5 channel
F635 SD Cy5 pixel intensity standard deviation
B635 Median median Cy5 feature background intensity
B635 Mean mean Cy5 feature background intensity
B635 SD Cy5 background pixel intensity standard deviation
% > B635+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
% > B635+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635 % Sat. percentage of pixel saturation within feature
F532 Median median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Median median feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
% > B532+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
% > B532+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
F532 % Sat. percentage of feature pixels at wavelength #2 (Cy3) that are saturated
Ratio of Medians (635/532) ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
Ratio of Means (635/532) ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
Median of Ratios (635/532) median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
Mean of Ratios (635/532) arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
Ratios SD (635/532) standard deviation of the log of pixel intensity ratios
Rgn Ratio (635/532) regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn R² (635/532) coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels number of feature pixels
B Pixels number of background pixels
Sum of Medians sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Sum of Means sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
VALUE Log ratio (635/532) - base two logarithm of the ratio of medians
F635 Median - B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532 Median - B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635 Mean - B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532 Mean - B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags A value of -100 means that this spot was bad. A value of -75 means that the ID for this spot is empty. A value of -50 means that this spot cannot be aligned during analysis. A value of 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality tests.
Normalize

Data table
ID_REF Block Column Row 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 Flags Normalize
1 1 1 1 2880 8260 60 575 615 197 494 502 151 40 18 0 769 784 129 496 510 158 84 43 0 0.297 0.42 0.8 0.458 4.364 1.44 0.036 32 170 354 409 -1.753 81 273 121 288 0 0
2 1 2 1 3080 8250 60 597 633 154 549 554 164 31 6 0 763 760 153 537 562 148 71 28 0 0.212 0.377 0.589 0.517 3.943 1.248 0.06 32 160 274 307 -2.235 48 226 84 223 0 0
3 1 3 1 3250 8260 130 834 874 276 472 486 148 87 58 0 1002 1267 2781 461 477 128 98 96 0 0.669 0.499 0.753 0.665 2.278 0.023 0.015 120 739 903 1208 -0.58 362 541 402 806 0 0
4 1 4 1 3450 8260 130 826 948 1396 472 485 147 81 58 0 1067 1626 4131 466 471 110 97 95 0 0.589 0.41 0.555 0.553 2.282 0.28 0.594 120 760 955 1636 -0.764 354 601 476 1160 0 0
5 1 5 1 3680 8260 120 1729 1814 632 508 522 166 99 96 0 2110 2245 1462 486 489 99 100 99 0 0.752 0.742 0.769 0.731 1.634 0.558 0.664 120 672 2845 3065 -0.411 1221 1624 1306 1759 0 0
6 1 6 1 3880 8260 120 1897 1902 537 550 582 223 95 93 0 2121 2099 470 500 546 864 94 37 0 0.831 0.846 0.868 0.811 1.923 0.372 0.301 120 639 2968 2951 -0.267 1347 1621 1352 1599 0 0
7 1 7 1 4070 8250 110 2504 2544 549 628 701 300 100 100 0 3189 3257 612 509 560 937 100 93 0 0.7 0.697 0.696 0.685 1.315 0.701 0.831 80 543 4556 4664 -0.515 1876 2680 1916 2748 0 0
8 1 8 1 4260 8260 110 2101 2155 428 614 666 278 100 100 0 2802 2751 470 483 522 562 100 96 0 0.641 0.679 0.653 0.672 1.363 0.677 0.78 80 566 3806 3809 -0.641 1487 2319 1541 2268 0 0
9 1 9 1 4460 8250 110 3047 3086 1039 581 625 238 100 100 0 3657 3619 536 495 539 242 100 100 0 0.78 0.802 0.772 0.766 1.365 0.837 0.776 80 566 5628 5629 -0.359 2466 3162 2505 3124 0 0
10 1 10 1 4650 8280 120 2937 2866 932 529 557 210 97 95 0 3262 3270 794 483 518 245 100 100 0 0.866 0.839 0.791 0.746 1.996 0.869 0.788 120 668 5187 5124 -0.207 2408 2779 2337 2787 0 0
11 1 11 1 4870 8270 110 2157 2183 469 491 513 166 100 100 0 3062 2949 560 474 501 215 100 100 0 0.644 0.684 0.685 0.676 1.363 0.657 0.826 80 571 4254 4167 -0.635 1666 2588 1692 2475 0 0
12 1 12 1 5070 8290 120 1817 1869 679 541 591 515 88 66 0 2492 2577 737 489 518 222 99 98 0 0.637 0.636 0.616 0.574 1.806 0.664 0.757 120 691 3279 3416 -0.651 1276 2003 1328 2088 0 0
13 1 1 2 2860 8450 110 476 486 155 486 493 181 11 1 0 518 531 101 472 481 131 21 2 0 -0.217 0 1.574 1.623 3.832 0.088 0.003 80 592 36 59 -10 46 0 59 -50 0
14 1 2 2 3060 8450 110 513 519 139 475 491 162 20 1 0 499 516 94 477 589 1249 0 0 0 1.727 1.128 1.409 1.622 5.446 487.495 0 80 602 60 83 0.788 38 22 44 39 -50 0
15 1 3 2 3260 8460 110 505 485 148 475 477 135 17 2 0 483 506 121 458 535 878 0 0 0 1.2 0.208 1.319 1.594 4.182 30.005 0.004 80 540 55 58 0.263 30 25 10 48 -50 0
16 1 4 2 3460 8460 110 456 487 158 481 488 146 16 6 0 497 511 96 463 495 385 1 0 0 -0.735 0.125 1.925 1.672 3.952 158.209 0 80 557 9 54 -25 34 6 48 -50 0
17 1 5 2 3680 8460 110 1188 1241 421 532 558 364 81 40 0 898 1032 1077 494 507 121 100 87 0 1.624 1.318 1.642 1.487 2.057 0.422 0.17 80 558 1060 1247 0.699 656 404 709 538 0 0
18 1 6 2 3870 8460 100 904 945 267 530 541 165 83 57 0 859 888 162 501 588 1231 0 0 0 1.045 1.072 0.98 0.955 2.356 1.41 0.27 80 484 732 802 0.063 374 358 415 387 0 0
19 1 7 2 4070 8460 120 5813 5655 1461 551 587 251 100 100 0 7971 7759 1663 506 583 1057 99 98 0 0.705 0.704 0.696 0.698 1.661 0.681 0.82 120 608 12727 12357 -0.505 5262 7465 5104 7253 0 0
20 1 8 2 4260 8460 120 5722 5623 1400 614 667 283 100 100 0 8166 7882 1707 511 570 852 98 98 0 0.667 0.68 0.697 0.685 1.573 0.678 0.853 120 582 12763 12380 -0.584 5108 7655 5009 7371 0 0

Total number of rows: 2880

Table truncated, full table size 513 Kbytes.




Supplementary data files not provided
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