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Sample GSM50342 Query DataSets for GSM50342
Status Public on Jan 02, 2006
Title Tissue_Unamp3
Sample type RNA
 
Channel 1
Source name PCA1, localized prostate adenocarcinoma tissue sample, 30 ug total RNA, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, Commercially available pool of benign prostate tissue total RNA, 30 ug total RNA, 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 1480 17140 120 1878 1816 391 921 924 135 94 93 0 1730 2004 1271 645 651 83 80 75 0 0.882 0.659 0.676 0.907 4.787 0.247 0.16 120 604 2042 2254 -0.181 957 1085 895 1359 0
Hs3-1-2-1 null 1660 17140 130 2104 2046 480 844 850 168 94 93 0 2018 2845 2240 644 648 86 83 81 0 0.917 0.546 0.648 0.866 5.25 0.228 0.281 120 595 2634 3403 -0.125 1260 1374 1202 2201 0
Hs3-1-3-1 null 1830 17130 110 1014 1198 796 854 881 171 50 45 0 716 861 385 637 646 86 48 41 0 2.025 1.536 6.368 4.405 8.525 -12.65 0.017 80 469 239 568 1.018 160 79 344 224 0
Hs3-1-4-1 null 2000 17150 120 1473 1527 562 970 1006 228 70 51 0 1384 2077 1446 635 644 90 90 85 0 0.672 0.386 0.643 0.617 5.607 0.084 0.021 120 582 1252 1999 -0.574 503 749 557 1442 0
Hs3-1-5-1 null 2190 17160 90 1053 1370 586 1018 1113 337 42 30 0 1864 2064 1031 635 643 94 90 88 0 0.028 0.246 0.714 0.607 5.87 -0.074 0.003 52 310 1264 1781 -5.134 35 1229 352 1429 0
Hs3-1-6-1 null 2350 17150 120 2350 2344 632 933 961 234 96 94 0 2172 3223 2345 632 639 85 93 89 0 0.92 0.545 0.618 0.828 3.666 0.299 0.438 120 523 2957 4002 -0.12 1417 1540 1411 2591 0
Hs3-1-7-1 -0.749281 2530 17150 120 4233 4290 1504 915 919 161 99 98 0 6989 10839 9484 644 652 89 95 95 0 0.523 0.331 0.377 0.488 3.873 0.183 0.533 120 516 9663 13570 -0.935 3318 6345 3375 10195 0
Hs3-1-8-1 null 2710 17140 130 2633 2746 994 864 865 157 96 95 0 2311 3339 2669 656 660 91 86 83 0 1.069 0.701 0.84 1.014 5.44 0.307 0.212 120 599 3424 4565 0.096 1769 1655 1882 2683 0
Hs3-1-9-1 null 2880 17140 120 2694 2883 1107 848 854 171 99 98 0 1249 2417 2314 646 647 86 83 72 0 3.061 1.149 1.903 2.46 4.112 0.629 0.473 120 538 2449 3806 1.614 1846 603 2035 1771 0
Hs3-1-10-1 null 3060 17140 130 2090 2042 970 821 827 164 82 71 0 1359 1853 1296 646 650 91 81 77 0 1.78 1.012 1.281 0.962 7.898 0.518 0.061 120 611 1982 2428 0.832 1269 713 1221 1207 0
Hs3-1-11-1 null 3240 17150 130 2018 2020 608 796 903 652 81 47 0 2175 3618 3128 654 1156 3535 31 15 0 0.803 0.413 0.545 0.671 4.449 0.172 0.248 120 601 2743 4188 -0.316 1222 1521 1224 2964 0
Hs3-1-12-1 null 3410 17140 100 2098 2074 694 1058 2218 2447 0 0 0 2249 4110 3494 695 3309 4669 35 8 0 0.669 0.298 0.385 0.411 3.073 0.459 0.573 80 433 2594 4431 -0.579 1040 1554 1016 3415 -50
Hs3-1-13-1 null 3590 17140 100 5448 5116 1420 4358 4127 2940 0 0 0 14112 12865 4207 5866 7336 6721 71 0 0 0.132 0.108 0.193 0.18 3.373 0.015 0.001 80 452 9336 7757 -2.919 1090 8246 758 6999 -50
Hs3-1-14-1 null 3760 17140 100 2228 2653 1249 981 1993 2222 27 2 0 1099 2548 2761 718 3129 5580 18 0 0 3.273 0.914 2.038 1.762 3.861 0.368 0.797 80 492 1628 3502 1.711 1247 381 1672 1830 -50
Hs3-1-15-1 -1.580195 3940 17170 90 2249 2284 417 1203 1320 466 96 61 0 4495 4434 1878 672 1085 3389 59 3 0 0.274 0.287 0.277 0.332 3.036 0.057 0.081 52 353 4869 4843 -1.87 1046 3823 1081 3762 0
Hs3-1-16-1 0.012425 4110 17150 120 4910 4976 1643 1090 1179 396 98 98 0 5235 5925 3994 653 688 240 90 86 0 0.834 0.737 0.676 1.043 4.256 0.516 0.588 120 630 8402 9158 -0.262 3820 4582 3886 5272 0
Hs3-1-17-1 0.768193 4290 17150 120 9577 9955 5376 1118 1304 616 100 96 0 9389 10559 8424 672 828 761 83 75 0 0.97 0.894 0.933 1.302 4.654 0.707 0.606 120 592 17176 18724 -0.043 8459 8717 8837 9887 0
Hs3-1-18-1 null 4470 17150 100 4043 3781 948 1901 3044 2852 10 0 0 5765 5714 3131 743 5083 8605 15 0 0 0.427 0.378 0.418 0.45 2.78 0.275 0.712 80 453 7164 6851 -1.229 2142 5022 1880 4971 -50
Hs3-1-19-1 null 4640 17150 100 7871 7172 1835 4358 5737 3872 40 0 0 25397 21217 7472 2511 12502 13269 75 0 0 0.153 0.15 0.177 0.155 2.594 0.152 0.197 80 480 26399 21520 -2.704 3513 22886 2814 18706 -50
Hs3-1-20-1 null 4820 17150 100 2398 2664 926 1310 2875 3442 0 0 0 1422 3195 3316 685 5486 10783 2 0 0 1.476 0.539 0.997 1.087 3.882 0.293 0.848 80 460 1825 3864 0.562 1088 737 1354 2510 -50

Total number of rows: 20000

Table truncated, full table size 3722 Kbytes.




Supplementary data files not provided
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