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Sample GSM50351 Query DataSets for GSM50351
Status Public on Jan 02, 2006
Title Tissue_WTA300ng3
Sample type RNA
 
Channel 1
Source name PCA1, localized prostate adenocarcinoma tissue sample, 300ng RNA WTA one PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, Commercially available pool of benign prostate tissue total RNA, 300ng RNA WTA one PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See MIAME Checklist
 
Submission date May 03, 2005
Last update date May 29, 2005
Contact name Scott Tomlins
E-mail(s) tomlinss@med.umich.edu
Phone 734-615-1417
Organization name University of Michigan
Department Pathology
Lab Chinnaiyan Lab
Street address 1400 E. Medical Center Dr., 5410 CCGC
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL2012
Series (1)
GSE2618 Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives

Data table header descriptions
ID_REF
VALUE Median of Ratios (635/532), normalized (lowess window 0.6), log base 2
X the X-coordiante in um of the centor of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in um 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 um of the feature-indicator
F635 Median median feature pixel intensity at wavelength #1 (635nm) (Cy5).
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 intesity 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 intesnsities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of featue pixels at wavelength #1 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm) (Cy3).
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 intensites, with the median background subtracted.
Mean of Ratios (635/532) the arithmetic mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the standard deviation of pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio.
Rgn R? the coefficient of determnination for the current regression value.
F Pixels the total number of feature pixels
B Pixels the total number of background pixels.
Sum of Medians the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) 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 substracted.
F532 Median - B532 the median featue 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.
Flags the type of flag associated with a feature. Features that could not be identified by Genepix are indicated with -50. Empty spots are indicated with -75.

Data table
ID_REF VALUE 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 R? F Pixels B Pixels Sum of Medians Sum of Means Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
Hs3-1-1-1 null 1800 17460 120 902 1182 897 166 172 65 93 89 0 1452 1869 1452 358 360 54 89 86 0 0.673 0.672 0.681 0.822 4.166 0.582 0.634 120 637 1830 2527 -0.572 736 1094 1016 1511 0
Hs3-1-2-1 -0.406193 1980 17460 120 2427 3359 2839 167 175 62 99 97 0 3296 4198 3618 357 360 58 93 90 0 0.769 0.831 0.814 1.038 4.417 0.762 0.627 120 550 5199 7033 -0.379 2260 2939 3192 3841 0
Hs3-1-3-1 null 2150 17480 60 262 274 113 162 174 69 65 37 0 1030 993 193 362 368 54 100 100 0 0.15 0.177 0.187 0.151 3.56 0.104 0.069 32 164 768 743 -2.74 100 668 112 631 0
Hs3-1-4-1 null 2320 17460 120 1065 1419 895 163 174 68 99 98 0 1586 2440 1898 346 348 58 89 86 0 0.727 0.6 0.656 0.859 4.269 0.463 0.614 120 674 2142 3350 -0.459 902 1240 1256 2094 0
Hs3-1-5-1 null 2500 17460 80 650 719 347 166 176 65 92 86 0 1628 1705 713 344 345 56 98 98 0 0.377 0.406 0.321 0.338 3.288 0.293 0.366 52 290 1768 1914 -1.408 484 1284 553 1361 0
Hs3-1-6-1 null 2660 17460 110 1172 1237 675 155 168 66 100 98 0 1841 1975 1023 339 342 59 100 98 0 0.677 0.661 0.651 0.698 2.772 0.584 0.563 80 492 2519 2718 -0.563 1017 1502 1082 1636 0
Hs3-1-7-1 -1.224342 2840 17460 130 5104 6929 5317 164 175 71 100 100 0 8690 12653 10416 336 342 58 95 95 0 0.591 0.549 0.486 0.587 4.115 0.453 0.599 120 640 13294 19082 -0.758 4940 8354 6765 12317 0
Hs3-1-8-1 null 3020 17460 120 859 1083 765 162 170 70 93 90 0 1328 1801 1264 334 337 69 92 90 0 0.701 0.628 0.592 0.693 3.765 0.528 0.532 120 624 1691 2388 -0.512 697 994 921 1467 0
Hs3-1-9-1 -0.636624 3190 17460 90 1908 2091 1275 171 182 79 100 100 0 2642 2730 1673 338 343 60 100 98 0 0.754 0.803 0.668 0.892 2.859 0.68 0.441 52 378 4041 4312 -0.408 1737 2304 1920 2392 0
Hs3-1-10-1 null 3370 17460 90 881 882 358 160 169 71 100 98 0 1826 1676 642 344 352 63 100 100 0 0.487 0.542 0.55 0.542 2.388 0.444 0.491 52 376 2203 2054 -1.039 721 1482 722 1332 0
Hs3-1-11-1 -1.166144 3550 17460 120 1040 1363 1038 172 299 443 65 49 0 2287 2625 2023 350 465 509 70 63 0 0.448 0.524 0.438 0.564 4.015 0.434 0.56 120 600 2805 3466 -1.158 868 1937 1191 2275 0
Hs3-1-12-1 null 3720 17460 100 730 1009 676 281 1298 1474 15 0 0 1422 1812 1195 388 1640 1895 35 0 0 0.434 0.511 0.431 0.482 4.04 0.722 0.62 80 432 1483 2152 -1.203 449 1034 728 1424 -50
Hs3-1-13-1 null 3900 17460 100 4237 4202 1419 2977 2427 1722 31 7 0 5229 5489 1910 3775 2942 2191 20 7 0 0.867 0.715 0.999 0.895 2.476 0.519 0.203 80 464 2714 2939 -0.207 1260 1454 1225 1714 -50
Hs3-1-14-1 null 4080 17460 100 323 467 413 177 863 1457 2 0 0 456 647 469 348 1216 1799 2 0 0 1.352 0.97 0.885 0.979 5.562 0.771 0.828 80 462 254 589 0.435 146 108 290 299 -50
Hs3-1-15-1 null 4240 17470 90 863 931 480 162 172 72 100 98 0 1810 1654 729 352 357 61 96 94 0 0.481 0.591 0.505 0.672 3.64 0.464 0.381 52 334 2159 2071 -1.057 701 1458 769 1302 0
Hs3-1-16-1 null 4430 17470 110 812 862 408 164 175 77 96 88 0 1621 1621 619 347 352 61 97 96 0 0.509 0.548 0.503 0.503 2.963 0.484 0.508 80 521 1922 1972 -0.975 648 1274 698 1274 0
Hs3-1-17-1 -0.092678 4600 17460 100 8158 8666 4185 165 189 109 100 100 0 7048 7830 4638 335 342 75 100 100 0 1.191 1.134 1.067 1.416 2.907 1.042 0.575 80 480 14706 15996 0.252 7993 6713 8501 7495 0
Hs3-1-18-1 -0.086385 4770 17460 80 4712 4297 1472 254 976 1438 94 76 0 4038 3905 1333 367 1171 1827 90 51 0 1.214 1.143 1.055 1.131 2.568 1.162 0.408 52 314 8129 7581 0.28 4458 3671 4043 3538 0
Hs3-1-19-1 null 4950 17470 100 3814 3816 1514 2806 2479 1856 15 6 0 4976 4661 1658 3196 3115 2582 16 2 0 0.566 0.689 0.575 0.559 4.439 0.282 0.008 80 462 2788 2475 -0.82 1008 1780 1010 1465 -50
Hs3-1-20-1 null 5130 17470 100 453 514 228 185 979 1556 0 0 0 672 744 355 367 1424 2037 0 0 0 0.879 0.873 0.942 0.867 3.237 0.735 0.837 80 433 573 706 -0.187 268 305 329 377 -50

Total number of rows: 20000

Table truncated, full table size 3668 Kbytes.




Supplementary data files not provided
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