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Sample GSM11011 Query DataSets for GSM11011
Status Public on Nov 15, 2003
Title FE5_FA3_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, 24hr fasting
Organism Sus scrofa
Extracted molecule total RNA
 
 
Description FE5_FA3_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 2500 8200 110 467 471 140 406 420 143 26 10 0 542 551 118 444 448 104 46 22 0 0.622 0.607 0.988 0.877 4.112 11.888 0.001 80 604 159 172 -0.684 61 98 65 107 -50 0
2 1 2 1 2700 8200 110 506 503 134 423 434 140 32 6 0 579 585 127 448 456 104 62 23 0 0.634 0.584 0.827 0.747 3.605 4.809 0.006 80 608 214 217 -0.658 83 131 80 137 -50 0
3 1 3 1 2900 8220 70 575 558 133 410 431 137 62 18 0 710 689 121 469 483 149 71 28 0 0.685 0.673 0.866 0.735 2.468 0.554 0.029 32 236 406 368 -0.547 165 241 148 220 0 0
4 1 4 1 3100 8210 90 539 522 140 392 404 137 51 15 0 748 757 144 434 444 104 96 76 0 0.468 0.402 0.487 0.425 2.613 0.768 0.068 52 414 461 453 -1.095 147 314 130 323 0 0
5 1 5 1 3330 8190 100 742 752 186 384 386 120 92 75 0 1203 1241 246 438 442 99 100 100 0 0.468 0.458 0.437 0.432 1.7 0.468 0.492 80 502 1123 1171 -1.096 358 765 368 803 0 0
6 1 6 1 3510 8210 110 697 722 184 370 385 128 90 71 0 1248 1236 258 424 434 106 100 100 0 0.397 0.433 0.466 0.411 1.928 0.401 0.378 80 559 1151 1164 -1.333 327 824 352 812 0 0
7 1 7 1 3710 8210 110 768 806 215 368 394 244 83 38 0 1576 1603 354 432 435 104 100 100 0 0.35 0.374 0.368 0.341 1.898 0.35 0.485 80 538 1544 1609 -1.516 400 1144 438 1171 0 0
8 1 8 1 3900 8210 110 766 788 219 380 396 234 77 37 0 1553 1559 381 439 444 112 100 100 0 0.346 0.364 0.361 0.332 1.904 0.435 0.23 80 566 1500 1528 -1.529 386 1114 408 1120 0 0
9 1 9 1 4100 8210 110 800 816 210 380 398 204 87 53 0 1166 1190 264 435 440 106 100 98 0 0.575 0.577 0.573 0.558 1.668 0.618 0.458 80 606 1151 1191 -0.799 420 731 436 755 0 0
10 1 10 1 4300 8210 110 829 860 218 383 393 149 97 80 0 1253 1241 221 441 447 109 100 100 0 0.549 0.596 0.591 0.544 1.749 0.649 0.591 80 621 1258 1277 -0.864 446 812 477 800 0 0
11 1 11 1 4530 8200 110 706 724 190 382 393 143 86 60 0 853 876 170 429 434 107 100 93 0 0.764 0.765 0.768 0.68 2.337 0.77 0.335 80 603 748 789 -0.388 324 424 342 447 0 0
12 1 12 1 4710 8230 100 706 697 163 380 388 144 82 60 0 837 833 215 418 425 104 95 83 0 0.778 0.764 0.781 0.752 2.38 0.772 0.323 80 510 745 732 -0.362 326 419 317 415 0 0
13 1 1 2 2500 8400 110 432 450 143 414 426 139 21 5 0 514 503 99 456 461 145 11 1 0 0.31 0.766 1.182 1.037 4.859 9.328 0.005 80 580 76 83 -1.688 18 58 36 47 -50 0
14 1 2 2 2700 8400 110 421 448 138 409 426 173 12 5 0 510 516 115 442 447 102 41 11 0 0.176 0.527 0.909 0.84 3.342 25.955 0.002 80 577 80 113 -2.503 12 68 39 74 -50 0
15 1 3 2 2900 8400 110 407 424 145 403 415 164 17 1 0 495 489 94 434 445 112 23 3 0 0.066 0.382 1.519 1.269 4.507 3.376 0.024 80 579 65 76 -3.931 4 61 21 55 -50 0
16 1 4 2 3100 8400 110 379 383 123 395 408 131 11 1 0 469 485 114 444 451 108 22 10 0 -0.64 -0.293 0.921 1.071 3.664 2.222 0.023 80 568 9 29 -16 25 -12 41 -50 0
17 1 5 2 3300 8400 110 427 436 144 387 401 142 25 5 0 510 512 93 437 447 116 30 6 0 0.548 0.653 1.052 1.045 3.109 0.126 0.006 80 571 113 124 -0.868 40 73 49 75 -50 0
18 1 6 2 3500 8400 110 347 366 135 371 380 136 13 3 0 478 483 101 429 439 119 31 1 0 -0.49 -0.093 1.818 1.106 5.237 3.027 0.018 80 572 25 49 -24 49 -5 54 -50 0
19 1 7 2 3710 8390 120 1537 1508 411 368 384 131 97 95 0 3312 3231 748 433 442 105 100 99 0 0.406 0.407 0.407 0.402 1.536 0.394 0.778 120 610 4048 3938 -1.3 1169 2879 1140 2798 0 0
20 1 8 2 3910 8410 120 1577 1561 449 381 393 124 96 95 0 3203 3124 700 433 442 108 100 100 0 0.432 0.438 0.433 0.413 1.63 0.434 0.807 120 606 3966 3871 -1.212 1196 2770 1180 2691 0 0

Total number of rows: 2880

Table truncated, full table size 514 Kbytes.




Supplementary data files not provided
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