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Sample GSM50337 Query DataSets for GSM50337
Status Public on Jan 02, 2006
Title WTA_LCM_PCA4
Sample type RNA
 
Channel 1
Source name LCM_PCA4, cancerous epithelium isolated by laser capture microdissection from a frozen prostate tissue sample, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, Commercially available pool of benign prostate tissue total RNA, WTA two PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See the 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 GPL2013
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
Hs6-1-1-1 null 1690 17990 110 1046 975 338 164 166 48 96 95 0 1198 1111 385 146 147 30 96 95 0 0.838 0.84 0.85 0.86 1.519 0.833 0.89 80 523 1934 1776 -0.254 882 1052 811 965 0
Hs6-1-2-1 null 1860 17990 100 1153 1131 485 161 165 54 100 97 0 1482 1359 567 140 144 50 100 97 0 0.739 0.796 0.781 0.796 1.695 0.809 0.919 80 438 2334 2189 -0.436 992 1342 970 1219 0
Hs6-1-3-1 null 2040 17990 80 236 225 59 158 163 58 53 21 0 354 338 86 142 144 28 90 88 0 0.368 0.342 0.393 0.306 3.868 0.396 0.216 52 300 290 263 -1.443 78 212 67 196 0
Hs6-1-4-1 null 2200 17980 90 857 843 209 163 168 56 100 98 0 1220 1201 243 138 144 44 100 100 0 0.641 0.64 0.653 0.62 1.301 0.679 0.872 52 385 1776 1743 -0.641 694 1082 680 1063 0
Hs6-1-5-1 null 2370 17990 90 467 468 107 166 171 55 100 98 0 646 656 147 137 145 48 100 100 0 0.591 0.582 0.587 0.572 1.558 0.579 0.712 52 361 810 821 -0.758 301 509 302 519 0
Hs6-1-6-1 null 2550 17990 100 1617 1503 510 159 167 71 98 97 0 1964 1755 616 138 142 35 100 100 0 0.798 0.831 0.85 0.843 1.606 0.819 0.919 80 449 3284 2961 -0.325 1458 1826 1344 1617 0
Hs6-1-7-1 0.120164 2730 17980 110 12375 10839 4410 164 170 69 100 100 0 10398 9296 3037 136 139 31 100 100 0 1.19 1.165 1.224 1.132 1.457 1.219 0.957 80 511 22473 19835 0.251 12211 10262 10675 9160 0
Hs6-1-8-1 null 2910 17980 110 1424 1380 481 166 170 53 100 100 0 1607 1555 496 136 139 28 100 100 0 0.855 0.856 0.855 0.83 1.218 0.88 0.952 80 497 2729 2633 -0.226 1258 1471 1214 1419 0
Hs6-1-9-1 -0.305095 3080 17980 110 3763 3767 1950 160 164 52 100 100 0 4166 4096 1895 136 138 27 100 100 0 0.894 0.911 0.911 0.868 1.401 0.942 0.963 80 483 7633 7567 -0.162 3603 4030 3607 3960 0
Hs6-1-10-1 null 3250 17980 110 1310 1259 453 154 159 51 97 96 0 1318 1255 393 136 138 26 100 100 0 0.978 0.987 0.976 0.907 1.491 1.015 0.931 80 496 2338 2224 -0.032 1156 1182 1105 1119 0
Hs6-1-11-1 null 3430 17980 110 1377 1307 535 159 165 52 97 95 0 2183 2038 750 136 136 27 100 100 0 0.595 0.604 0.597 0.555 1.45 0.619 0.936 80 511 3265 3050 -0.749 1218 2047 1148 1902 0
Hs6-1-12-1 null 3610 17980 110 1090 1013 448 153 158 51 97 95 0 1242 1135 445 135 134 26 97 97 0 0.846 0.86 0.882 0.816 1.472 0.89 0.916 80 512 2044 1860 -0.241 937 1107 860 1000 0
Hs6-1-13-1 -0.145968 3770 17980 90 2358 2174 734 151 166 81 100 98 0 2352 2043 729 136 146 66 96 96 0 0.996 1.061 1.016 1.14 1.543 1.066 0.922 52 353 4423 3930 -0.006 2207 2216 2023 1907 0
Hs6-1-14-1 null 3930 17990 90 1613 1478 670 169 194 137 92 86 0 1928 1694 726 149 182 149 92 90 0 0.812 0.847 0.849 0.833 1.569 0.875 0.895 52 367 3223 2854 -0.301 1444 1779 1309 1545 0
Hs6-1-15-1 0.050936 4130 17980 110 2618 2519 885 158 171 93 100 100 0 2343 2179 669 140 155 96 100 98 0 1.117 1.158 1.161 1.143 1.265 1.19 0.946 80 528 4663 4400 0.159 2460 2203 2361 2039 0
Hs6-1-16-1 null 4300 17980 100 789 774 289 156 160 47 100 96 0 836 829 309 130 134 28 96 96 0 0.897 0.884 0.893 0.961 2.374 0.893 0.872 80 440 1339 1317 -0.157 633 706 618 699 0
Hs6-1-17-1 -0.200304 4480 17980 100 2260 2056 919 155 157 47 98 97 0 2280 2057 822 127 129 27 98 97 0 0.978 0.985 0.98 0.897 1.615 1.014 0.943 80 440 4258 3831 -0.033 2105 2153 1901 1930 0
Hs6-1-18-1 null 4650 17980 100 613 592 231 159 164 54 92 87 0 812 725 260 130 131 27 100 97 0 0.666 0.728 0.764 0.664 2.12 0.759 0.824 80 428 1136 1028 -0.587 454 682 433 595 0
Hs6-1-19-1 -1.072181 4820 17980 110 1710 1611 608 153 161 57 100 98 0 2930 2751 1080 128 132 38 100 100 0 0.556 0.556 0.535 0.556 1.489 0.547 0.927 80 471 4359 4081 -0.848 1557 2802 1458 2623 0
Hs6-1-20-1 null 5000 17980 120 942 1358 924 155 161 52 97 96 0 957 1216 803 124 129 35 99 98 0 0.945 1.102 1.105 1.082 1.759 1.126 0.943 120 557 1620 2295 -0.082 787 833 1203 1092 0

Total number of rows: 20000

Table truncated, full table size 3620 Kbytes.




Supplementary data files not provided
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