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Sample GSM50347 Query DataSets for GSM50347
Status Public on Jan 02, 2006
Title Tissue_WTA75ng
Sample type RNA
 
Channel 1
Source name PCA1, localized prostate adenocarcinoma tissue sample, 75ng 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, 75ng 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 -0.969767 1350 17290 80 1100 1130 543 194 212 95 94 88 0 2112 1799 904 658 665 94 80 78 0 0.623 0.82 0.643 0.564 3.125 0.56 0.317 52 334 2360 2077 -0.682 906 1454 936 1141 0
Hs3-1-2-1 -0.421252 1520 17290 80 1704 1796 1002 208 225 98 100 98 0 2140 1892 997 646 651 83 80 80 0 1.001 1.274 1.045 1.109 3.843 1.226 0.328 52 328 2990 2834 0.002 1496 1494 1588 1246 0
Hs3-1-3-1 null 1700 17310 50 269 289 118 224 228 94 41 16 0 1477 1444 183 576 594 143 100 100 0 0.05 0.075 0.116 0.114 2.293 0.044 0.048 12 104 946 933 -4.324 45 901 65 868 0
Hs3-1-4-1 -1.553815 1870 17300 80 1035 1048 497 208 214 88 96 88 0 2171 1824 891 649 648 94 80 80 0 0.543 0.715 0.428 0.436 2.132 0.485 0.322 52 340 2349 2015 -0.88 827 1522 840 1175 0
Hs3-1-5-1 null 2030 17300 50 575 589 198 239 271 142 91 75 0 1770 1753 242 600 652 233 100 100 0 0.287 0.304 0.287 0.265 1.821 0.151 0.133 12 104 1506 1503 -1.8 336 1170 350 1153 0
Hs3-1-6-1 -1.178254 2210 17300 60 841 784 324 224 238 112 87 75 0 1845 1616 575 641 625 106 87 84 0 0.512 0.574 0.485 0.366 2.376 0.364 0.245 32 176 1821 1535 -0.964 617 1204 560 975 0
Hs3-1-7-1 -1.232572 2380 17280 110 4002 4165 2472 203 215 93 100 100 0 5113 5421 4294 648 648 95 85 83 0 0.851 0.83 0.795 1.043 4.603 0.616 0.492 80 554 8264 8735 -0.233 3799 4465 3962 4773 0
Hs3-1-8-1 -0.607443 2560 17280 80 1126 1153 608 201 211 91 96 88 0 1680 1646 925 659 663 91 76 73 0 0.906 0.965 0.747 0.804 2.908 0.656 0.317 52 334 1946 1939 -0.142 925 1021 952 987 0
Hs3-1-9-1 -0.391923 2730 17280 70 1600 1692 754 210 229 109 100 96 0 1894 1496 859 642 647 87 71 71 0 1.11 1.735 1.011 1.378 4.886 1.343 0.2 32 236 2642 2336 0.151 1390 1252 1482 854 0
Hs3-1-10-1 null 2940 17290 50 504 473 201 214 249 122 66 50 0 1559 1515 251 601 677 276 100 100 0 0.303 0.283 0.282 0.192 4.268 0.151 0.117 12 104 1248 1173 -1.724 290 958 259 914 0
Hs3-1-11-1 -1.172501 3090 17280 80 1003 1059 587 197 208 89 92 86 0 2038 1716 803 638 638 83 82 80 0 0.576 0.8 0.54 0.48 3.458 0.572 0.243 52 323 2206 1940 -0.797 806 1400 862 1078 0
Hs3-1-12-1 -0.476469 3280 17280 50 1597 1491 384 363 500 415 100 66 0 2050 1825 621 620 760 419 83 75 0 0.863 0.936 0.957 0.883 2.115 0.625 0.158 12 104 2664 2333 -0.213 1234 1430 1128 1205 0
Hs3-1-13-1 null 3450 17280 100 1547 1499 493 616 889 719 67 11 0 2393 2093 793 746 1328 824 78 50 0 0.565 0.656 0.587 0.557 2.747 0.534 0.014 80 462 2578 2230 -0.823 931 1647 883 1347 -50
Hs3-1-14-1 null 3620 17270 100 392 738 771 217 435 590 25 18 0 642 907 650 631 863 623 21 13 0 15.909 1.888 0.768 0.951 4.721 1.094 0.527 80 486 186 797 3.992 175 11 521 276 -50
Hs3-1-15-1 null 3790 17280 60 644 717 324 206 216 92 93 93 0 1759 1487 732 628 628 83 78 78 0 0.387 0.595 0.31 0.315 1.894 0.144 0.056 32 176 1569 1370 -1.369 438 1131 511 859 0
Hs3-1-16-1 -0.848034 3960 17280 70 797 787 256 190 215 104 93 93 0 1669 1395 672 613 630 129 78 75 0 0.575 0.763 0.58 0.533 2.156 0.296 0.206 32 236 1663 1379 -0.799 607 1056 597 782 0
Hs3-1-17-1 -0.078625 4140 17270 100 4540 4576 2857 199 214 101 100 100 0 2592 2792 1950 590 595 99 78 75 0 2.168 1.988 1.669 1.911 3.969 2.152 0.408 80 515 6343 6579 1.117 4341 2002 4377 2202 0
Hs3-1-18-1 0.230251 4320 17260 90 3094 3064 1473 288 1005 1628 76 40 0 2105 1787 940 617 1264 1492 48 0 0 1.886 2.373 1.873 2.768 4.751 1.661 0.474 52 381 4294 3946 0.915 2806 1488 2776 1170 0
Hs3-1-19-1 null 4500 17270 100 2880 2843 1154 1759 2745 2488 12 0 0 3612 3269 1341 1014 2727 2334 65 0 0 0.431 0.481 0.542 0.433 3.599 1.26 0.404 80 450 3719 3339 -1.213 1121 2598 1084 2255 -50
Hs3-1-20-1 null 4670 17260 100 318 333 152 224 1013 1939 0 0 0 564 567 196 609 1299 1736 0 0 0 -2.089 -2.595 0.689 0.652 6.448 1.086 0.868 80 490 49 67 Error 94 -45 109 -42 -50

Total number of rows: 20000

Table truncated, full table size 3592 Kbytes.




Supplementary data files not provided
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