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Sample GSM11012 Query DataSets for GSM11012
Status Public on Nov 15, 2003
Title FA5_FE3_bot
Sample type RNA
 
Channel 1
Source name Porcine liver, 5 weeks, male, Yorkshire x Landrace, 24hr fasting
Organism Sus scrofa
Extracted molecule total RNA
 
Channel 2
Source name Porcine liver, 5 weeks, male, Yorkshire x Landrace, fed
Organism Sus scrofa
Extracted molecule total RNA
 
 
Description FA5_FE3_bot
 
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 2620 50200 120 1090 1094 351 297 320 191 95 89 0 1388 1393 361 359 369 105 98 95 0 0.771 0.771 0.742 0.749 2.205 0.845 0.597 120 706 1822 1831 -0.376 793 1029 797 1034 0 0
2 1 2 1 2820 50200 110 1148 1184 304 284 322 244 100 93 0 1624 1589 301 342 363 111 100 100 0 0.674 0.722 0.688 0.703 1.477 0.757 0.585 80 566 2146 2147 -0.569 864 1282 900 1247 0 0
3 1 3 1 3010 50180 110 1008 1040 257 280 313 229 100 90 0 1665 1645 303 346 362 126 100 100 0 0.552 0.585 0.582 0.569 1.487 0.628 0.573 80 611 2047 2059 -0.857 728 1319 760 1299 0 0
4 1 4 1 3220 50190 110 1042 1036 271 289 305 189 98 95 0 1501 1490 225 346 360 100 100 100 0 0.652 0.653 0.622 0.619 1.613 0.672 0.573 80 624 1908 1891 -0.617 753 1155 747 1144 0 0
5 1 5 1 3440 50170 120 2216 2212 510 278 307 207 100 99 0 2461 2371 528 338 347 89 100 99 0 0.913 0.951 0.918 0.957 1.54 0.947 0.828 120 649 4061 3967 -0.132 1938 2123 1934 2033 0 0
6 1 6 1 3630 50190 120 2484 2366 618 285 313 208 99 99 0 2689 2533 707 335 342 84 99 99 0 0.934 0.947 0.944 0.949 1.597 0.935 0.844 120 622 4553 4279 -0.098 2199 2354 2081 2198 0 0
7 1 7 1 3820 50180 110 4978 5013 1070 281 296 123 100 100 0 5099 4986 992 334 339 87 100 100 0 0.986 1.017 1.023 1.013 1.265 1.023 0.899 80 549 9462 9384 -0.021 4697 4765 4732 4652 0 0
8 1 8 1 4020 50190 110 4815 4763 818 274 301 171 100 100 0 4552 4491 836 332 344 116 100 100 0 1.076 1.079 1.074 1.084 1.22 1.06 0.886 80 561 8761 8648 0.106 4541 4220 4489 4159 0 0
9 1 9 1 4210 50200 120 2523 2388 724 260 425 2408 42 0 0 3871 3750 1143 340 473 2067 88 31 0 0.641 0.624 0.617 0.651 1.916 0.605 0.839 120 657 5794 5538 -0.642 2263 3531 2128 3410 0 0
10 1 10 1 4430 50200 120 2623 2487 880 232 392 2405 49 0 0 4192 4050 1057 308 436 2048 94 36 0 0.616 0.603 0.596 0.548 1.644 0.937 0.429 120 666 6275 5997 -0.7 2391 3884 2255 3742 0 0
11 1 11 1 4640 50190 120 2061 2059 653 203 319 1376 75 9 0 3250 3223 882 274 288 142 100 100 0 0.624 0.629 0.635 0.614 1.441 0.632 0.812 120 624 4834 4805 -0.68 1858 2976 1856 2949 0 0
12 1 12 1 4840 50200 120 1906 1873 599 198 283 1292 78 5 0 3101 3042 794 265 281 144 100 100 0 0.602 0.603 0.608 0.581 1.557 0.598 0.856 120 665 4544 4452 -0.732 1708 2836 1675 2777 0 0
13 1 1 2 2630 50380 90 657 654 190 293 345 322 59 9 0 1080 1093 198 349 364 106 100 100 0 0.498 0.485 0.512 0.48 1.656 1.25 0.113 52 390 1095 1105 -1.006 364 731 361 744 0 0
14 1 2 2 2830 50400 110 591 616 199 288 330 304 50 10 0 1010 1041 218 349 358 106 100 100 0 0.458 0.474 0.419 0.426 1.942 0.657 0.201 80 556 964 1020 -1.125 303 661 328 692 0 0
15 1 3 2 3020 50400 90 534 552 225 277 305 232 51 13 0 915 931 227 343 353 104 98 96 0 0.449 0.468 0.39 0.393 2.457 0.795 0.091 52 390 829 863 -1.154 257 572 275 588 0 0
16 1 4 2 3230 50400 90 478 527 254 283 321 485 9 1 0 882 884 169 332 344 91 100 100 0 0.355 0.442 0.42 0.366 2.509 29.886 0.004 52 388 745 796 -1.496 195 550 244 552 0 0
17 1 5 2 3440 50370 100 679 656 185 299 325 440 31 0 0 938 946 190 341 359 152 100 96 0 0.637 0.59 0.578 0.525 2.254 0.628 0.201 80 508 977 962 -0.652 380 597 357 605 0 0
18 1 6 2 3630 50380 110 687 692 181 299 324 245 80 25 0 959 978 175 349 360 104 100 100 0 0.636 0.625 0.597 0.595 1.809 1.309 0.173 80 514 998 1022 -0.653 388 610 393 629 0 0
19 1 7 2 3830 50380 130 6574 6434 1321 278 299 194 99 99 0 7269 7197 980 332 339 85 100 100 0 0.908 0.897 0.925 0.858 1.488 0.925 0.907 120 658 13233 13021 -0.14 6296 6937 6156 6865 0 0
20 1 8 2 4030 50400 120 6715 6391 1592 274 301 220 99 98 0 6879 6560 1544 332 347 123 99 99 0 0.984 0.982 0.97 0.961 1.954 0.993 0.852 120 560 12988 12345 -0.024 6441 6547 6117 6228 0 0

Total number of rows: 2880

Table truncated, full table size 518 Kbytes.




Supplementary data files not provided
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