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Sample GSM50168 Query DataSets for GSM50168
Status Public on Jan 02, 2006
Title WTA_FFPE_NOR1
Sample type RNA
 
Channel 1
Source name Formalin-fixed paraffin embedded prostate tissue containing benign prostate, WTA two PCR, 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 1780 17990 110 1220 1169 389 197 199 67 98 96 0 1052 1005 330 101 103 21 98 97 0 1.076 1.075 1.046 1.079 1.703 1.123 0.897 80 541 1974 1876 0.105 1023 951 972 904 0
Hs6-1-2-1 null 1950 18000 100 938 925 330 183 188 63 98 93 0 1156 1079 437 100 101 20 100 100 0 0.715 0.758 0.752 0.743 1.694 0.754 0.87 80 447 1811 1721 -0.484 755 1056 742 979 0
Hs6-1-3-1 null 2130 17990 60 270 275 82 182 189 61 62 40 0 275 234 82 102 105 24 87 78 0 0.509 0.705 0.739 0.827 4.081 1.384 0.202 32 176 261 225 -0.975 88 173 93 132 0
Hs6-1-4-1 null 2310 18000 100 1444 1293 543 189 195 65 97 95 0 964 914 393 97 99 21 100 97 0 1.448 1.351 1.376 1.311 1.634 1.377 0.878 80 448 2122 1921 0.534 1255 867 1104 817 0
Hs6-1-5-1 null 2470 18010 80 551 533 187 188 196 62 94 86 0 517 451 167 101 102 23 94 90 0 0.873 0.986 0.972 0.965 1.59 1.067 0.775 52 280 779 695 -0.197 363 416 345 350 0
Hs6-1-6-1 null 2650 18010 110 1306 1247 478 183 191 63 100 98 0 1648 1509 624 101 102 24 100 97 0 0.726 0.756 0.741 0.787 1.679 0.747 0.888 80 488 2670 2472 -0.462 1123 1547 1064 1408 0
Hs6-1-7-1 -0.198444 2830 18010 120 7143 6283 2694 187 194 63 99 99 0 7845 7186 3025 98 101 22 100 100 0 0.898 0.86 0.848 0.814 1.808 0.861 0.94 120 562 14703 13184 -0.155 6956 7747 6096 7088 0
Hs6-1-8-1 null 3010 18010 100 994 1012 363 185 193 64 96 95 0 1042 999 400 98 100 21 98 98 0 0.857 0.918 0.916 0.916 1.784 0.919 0.874 80 388 1753 1728 -0.223 809 944 827 901 0
Hs6-1-9-1 -0.151825 3180 18010 120 2672 2764 1888 199 205 63 99 98 0 2512 2743 1909 99 101 21 100 100 0 1.025 0.97 0.965 0.928 1.498 0.978 0.955 120 556 4886 5209 0.035 2473 2413 2565 2644 0
Hs6-1-10-1 null 3360 18010 110 698 682 256 195 199 62 97 93 0 625 596 194 99 101 20 100 100 0 0.956 0.98 0.949 0.88 1.678 1.098 0.787 80 477 1029 984 -0.065 503 526 487 497 0
Hs6-1-11-1 null 3530 18010 110 1342 1328 541 192 198 66 100 100 0 1643 1568 687 101 104 23 100 100 0 0.746 0.774 0.765 0.785 1.456 0.776 0.913 80 497 2692 2603 -0.423 1150 1542 1136 1467 0
Hs6-1-12-1 null 3710 18010 110 698 755 294 195 202 65 98 92 0 739 714 308 99 102 22 100 100 0 0.786 0.911 0.941 0.916 1.445 0.936 0.895 80 511 1143 1175 -0.348 503 640 560 615 0
Hs6-1-13-1 null 3880 18020 100 1636 1504 718 188 195 67 100 98 0 1879 1669 850 99 99 20 100 100 0 0.813 0.838 0.852 0.858 1.636 0.824 0.921 80 428 3228 2886 -0.298 1448 1780 1316 1570 0
Hs6-1-14-1 -0.354257 4050 18020 100 1850 1787 917 194 200 64 98 97 0 1955 1942 992 100 101 20 100 100 0 0.893 0.865 0.851 0.798 1.503 0.875 0.93 80 440 3511 3435 -0.164 1656 1855 1593 1842 0
Hs6-1-15-1 0.049682 4230 18020 110 2260 2051 845 195 205 68 98 98 0 1921 1755 678 100 102 22 100 100 0 1.134 1.121 1.123 1.058 1.367 1.139 0.926 80 498 3886 3511 0.181 2065 1821 1856 1655 0
Hs6-1-16-1 null 4400 18030 100 647 629 212 189 196 64 97 95 0 626 588 209 101 101 20 100 100 0 0.872 0.903 0.909 0.877 1.706 0.95 0.764 80 440 983 927 -0.197 458 525 440 487 0
Hs6-1-17-1 0.124864 4580 18030 100 2658 2416 984 192 197 64 100 100 0 2144 1937 940 99 100 19 100 100 0 1.206 1.21 1.177 1.284 1.563 1.156 0.928 80 440 4511 4062 0.27 2466 2045 2224 1838 0
Hs6-1-18-1 null 4750 18030 100 661 665 253 198 201 64 95 92 0 610 589 243 101 101 20 96 96 0 0.91 0.957 0.945 0.959 1.744 1.009 0.832 80 440 972 955 -0.137 463 509 467 488 0
Hs6-1-19-1 0.228251 4930 18030 110 4510 4190 1670 199 202 62 100 100 0 3725 3389 1339 100 101 20 100 100 0 1.189 1.213 1.193 1.203 1.25 1.225 0.963 80 496 7936 7280 0.25 4311 3625 3991 3289 0
Hs6-1-20-1 null 5100 18030 110 1209 1309 569 190 199 65 100 100 0 1288 1308 626 99 101 20 100 100 0 0.857 0.926 0.93 0.945 1.412 0.922 0.929 80 491 2208 2328 -0.223 1019 1189 1119 1209 0

Total number of rows: 20000

Table truncated, full table size 3565 Kbytes.




Supplementary data files not provided
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