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Sample GSM50348 Query DataSets for GSM50348
Status Public on Jan 02, 2006
Title Tissue_WTA150ng
Sample type RNA
 
Channel 1
Source name PCA1, localized prostate adenocarcinoma tissue sample, 150ng 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, 150ng 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 -0.487786 1330 17710 80 1916 1997 763 180 187 77 100 100 0 2408 2682 1367 564 572 98 100 98 0 0.941 0.858 1.015 1.024 2.404 0.63 0.465 52 334 3580 3935 -0.087 1736 1844 1817 2118 0
Hs3-1-2-1 -0.040397 1500 17700 90 4775 5312 2729 182 190 77 100 100 0 2864 4148 2870 552 574 142 92 90 0 1.987 1.427 1.607 1.69 2.054 1.125 0.552 52 379 6905 8726 0.99 4593 2312 5130 3596 0
Hs3-1-3-1 null 1660 17720 50 376 403 123 199 211 90 83 50 0 1385 1357 292 539 546 125 100 91 0 0.209 0.249 0.214 0.272 2.498 0.099 0.077 12 104 1023 1022 -2.257 177 846 204 818 0
Hs3-1-4-1 -1.275762 1850 17710 110 1443 1754 1085 176 181 73 100 98 0 2511 2940 1721 518 524 86 98 93 0 0.636 0.652 0.571 0.709 3.457 0.566 0.562 80 598 3260 4000 -0.654 1267 1993 1578 2422 0
Hs3-1-5-1 null 2030 17710 80 858 878 429 178 188 85 98 96 0 2118 2044 834 528 529 75 100 100 0 0.428 0.462 0.365 0.456 2.665 0.349 0.413 52 286 2270 2216 -1.225 680 1590 700 1516 0
Hs3-1-6-1 -0.622978 2190 17700 90 1872 1831 679 159 175 75 100 100 0 2649 2338 971 524 525 79 100 100 0 0.806 0.922 0.943 1.036 2.124 0.782 0.578 52 362 3838 3486 -0.311 1713 2125 1672 1814 0
Hs3-1-7-1 -1.682999 2370 17700 120 5937 8094 7484 175 183 81 100 100 0 7612 12680 12282 510 513 80 94 94 0 0.811 0.651 0.556 0.617 3.39 0.54 0.549 120 603 12864 20089 -0.302 5762 7102 7919 12170 0
Hs3-1-8-1 null 2550 17690 100 1183 1408 852 179 187 74 100 97 0 1475 2108 1433 498 506 82 95 90 0 1.028 0.763 0.828 0.963 3.26 0.595 0.513 80 467 1981 2839 0.039 1004 977 1229 1610 0
Hs3-1-9-1 0.058199 2720 17690 90 2103 2663 1658 184 191 77 100 100 0 2081 2693 1747 500 516 127 98 90 0 1.214 1.13 1.472 1.391 3.487 1.052 0.47 52 394 3500 4672 0.28 1919 1581 2479 2193 0
Hs3-1-10-1 null 2890 17690 70 1023 1031 287 175 190 85 100 100 0 1776 1676 569 499 509 107 96 93 0 0.664 0.727 0.645 0.837 2.36 0.506 0.476 32 236 2125 2033 -0.591 848 1277 856 1177 0
Hs3-1-11-1 -1.294108 3070 17690 90 2442 2488 1345 178 188 82 100 100 0 3622 3791 1856 498 497 77 98 98 0 0.725 0.701 0.643 0.655 2.701 0.615 0.499 52 414 5388 5603 -0.465 2264 3124 2310 3293 0
Hs3-1-12-1 -1.303556 3250 17690 80 1323 1442 799 232 834 1202 42 9 0 2264 2509 1138 508 967 1110 73 40 0 0.621 0.605 0.536 0.575 3.276 0.602 0.238 52 307 2847 3211 -0.687 1091 1756 1210 2001 0
Hs3-1-13-1 null 3420 17680 100 5206 5463 1369 1076 2343 2313 97 31 0 5669 5898 1322 687 2465 2320 100 60 0 0.829 0.842 0.836 0.829 1.265 0.854 0.484 80 435 9112 9598 -0.271 4130 4982 4387 5211 -50
Hs3-1-14-1 null 3600 17670 100 326 321 118 224 1226 2049 0 0 0 555 566 124 520 1554 2078 0 0 0 2.914 2.109 1.474 1.328 5.815 0.98 0.866 80 474 137 143 1.543 102 35 97 46 -50
Hs3-1-15-1 null 3770 17670 80 1059 1285 634 172 183 77 100 98 0 1798 1875 811 498 505 77 94 94 0 0.682 0.808 0.708 0.876 2.973 0.657 0.395 52 306 2187 2490 -0.552 887 1300 1113 1377 0
Hs3-1-16-1 null 3950 17680 100 929 955 505 174 187 79 96 92 0 1564 1591 733 499 502 79 92 87 0 0.709 0.715 0.622 0.662 2.748 0.623 0.51 80 450 1820 1873 -0.496 755 1065 781 1092 0
Hs3-1-17-1 -0.296483 4120 17670 100 8783 9874 5849 189 215 139 100 100 0 6906 7245 4846 495 502 85 95 92 0 1.341 1.435 1.483 1.749 3.082 1.465 0.542 80 462 15005 16435 0.423 8594 6411 9685 6750 0
Hs3-1-18-1 -0.093823 4290 17660 90 7434 6767 2744 231 441 500 100 96 0 3686 4095 2271 516 676 443 94 82 0 2.272 1.826 1.629 2.136 3.231 1.751 0.515 52 299 10373 10115 1.184 7203 3170 6536 3579 0
Hs3-1-19-1 -1.020385 4470 17670 200 6917 6690 1687 197 311 379 100 100 0 8049 7824 1760 509 630 448 99 99 0 0.891 0.888 0.892 0.886 1.485 0.878 0.693 316 1760 14260 13808 -0.166 6720 7540 6493 7315 0
Hs3-1-20-1 -0.739825 4630 17680 60 1884 2433 1934 234 280 195 96 84 0 2894 3457 2118 544 552 98 100 96 0 0.702 0.755 0.88 0.673 4.416 0.734 0.283 32 132 4000 5112 -0.51 1650 2350 2199 2913 0

Total number of rows: 20000

Table truncated, full table size 3652 Kbytes.




Supplementary data files not provided
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