NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM50354 Query DataSets for GSM50354
Status Public on Jan 02, 2006
Title ThreeRound_PCR
Sample type RNA
 
Channel 1
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA three PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA three PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See MIAME checklist
 
Submission date May 04, 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 normalized (mean of the Median of Ratios of included features = 1), log base 2, (meanF635-B635)/(meanF532-B532)
X the X-coordinate in um of the center 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 (635 nm) (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 intensity 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 intensities more than two standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature ixels 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 pixel 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 deviation above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature ixels 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 intensities, 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 determination 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 subtracted.
F532 Median - B532 the median feature 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 1450 17790 80 3487 3441 1194 1303 1370 518 90 84 0 5623 5330 2049 3775 3962 896 67 51 0 1.182 1.375 1.026 1.066 1.755 0.782 0.654 52 288 4032 3693 0.241 2184 1848 2138 1555 0
Hs6-1-2-1 0.061300187 1600 17780 110 3974 3839 1845 1301 1335 466 85 81 0 5618 5173 2911 4071 4189 1009 61 42 0 1.728 2.303 1.083 0.859 4.469 0.818 0.512 80 439 4220 3640 0.789 2673 1547 2538 1102 0
Hs6-1-3-1 null 1770 17770 100 1219 1238 406 1237 1278 400 16 3 0 3099 2569 1495 4573 4412 931 1 0 0 0.012 0 0.127 0.116 4.947 0.073 0.04 80 466 -1492 -2003 -6.356 -18 -1474 1 -2004 -50
Hs6-1-4-1 0.053671536 1980 17770 110 4342 4364 1273 1258 1315 463 100 100 0 6426 5994 1695 4467 4396 995 71 48 0 1.574 2.034 1.551 1.813 2.231 1.102 0.555 80 484 5043 4633 0.655 3084 1959 3106 1527 0
Hs6-1-5-1 null 2120 17770 100 1816 1839 680 1129 1195 495 60 30 0 3677 3059 1663 4092 4121 953 6 0 0 -1.655 -0.687 1.555 0.933 6.925 0.209 0.059 80 369 272 -323 Error 687 -415 710 -1033 -50
Hs6-1-6-1 0.475908064 2290 17780 110 7219 6468 3313 1066 1135 574 87 78 0 8730 7513 4069 4075 4025 929 72 70 0 1.322 1.571 1.213 1.192 2.735 1.057 0.813 80 442 10808 8840 0.403 6153 4655 5402 3438 0
Hs6-1-7-1 0.070915629 2450 17770 110 12032 15300 12556 1196 1445 1312 85 75 0 12747 15938 13549 3983 4127 1353 68 67 0 1.236 1.18 1.036 1.269 1.904 1.005 0.935 80 507 19600 26059 0.306 10836 8764 14104 11955 0
Hs6-1-8-1 null 2650 17770 100 2473 3045 1825 1261 1537 1264 47 25 0 4303 4181 2742 3888 4046 1329 28 20 0 2.92 6.089 1.124 0.91 3.042 0.735 0.448 80 458 1627 2077 1.546 1212 415 1784 293 -50
Hs6-1-9-1 0.096362668 2820 17770 110 6242 8129 6157 1266 1369 618 83 80 0 7186 8888 6813 4013 4062 976 67 60 0 1.568 1.408 1.149 1.037 3.445 1.033 0.879 80 496 8149 11738 0.649 4976 3173 6863 4875 0
Hs6-1-10-1 null 3000 17770 100 2397 2569 967 1349 1396 603 70 45 0 3714 3700 1670 4046 4055 981 21 8 0 -3.157 -3.526 1.163 0.868 7.549 0.646 0.153 80 438 716 874 Error 1048 -332 1220 -346 -50
Hs6-1-11-1 null 3160 17770 100 3517 3916 1908 1415 1470 606 82 67 0 4889 4674 2697 4143 4134 962 48 33 0 2.818 4.71 1.316 1.378 4.761 0.947 0.516 80 436 2848 3032 1.495 2102 746 2501 531 0
Hs6-1-12-1 null 3350 17760 100 2433 2602 981 1450 1604 767 58 31 0 4190 3692 1880 4295 4251 1004 16 5 0 -9.362 -1.91 1.684 1.61 6.3 0.557 0.298 80 484 878 549 Error 983 -105 1152 -603 -50
Hs6-1-13-1 0.95082067 3520 17770 110 6342 5523 2786 1496 1625 800 78 71 0 7689 6419 3808 4446 4400 919 66 65 0 1.494 2.041 1.248 0.92 3.27 1.017 0.688 80 484 8089 6000 0.579 4846 3243 4027 1973 0
Hs6-1-14-1 null 3690 17780 110 4786 5236 2733 1380 1528 686 85 81 0 6639 6271 3810 4356 4314 873 60 55 0 1.492 2.014 1.18 1.111 3.134 0.978 0.676 80 494 5689 5771 0.577 3406 2283 3856 1915 0
Hs6-1-15-1 null 3860 17780 110 3675 3795 1494 1607 1652 611 86 72 0 5341 4844 2398 4486 4418 968 47 30 0 2.419 6.112 1.581 1.108 3.796 0.926 0.385 80 493 2923 2546 1.274 2068 855 2188 358 0
Hs6-1-16-1 null 4050 17790 70 2813 2789 957 1620 1811 742 62 34 0 4626 4121 1626 3949 3913 1000 43 0 0 1.762 6.797 1.101 0.79 5.464 0.485 0.226 32 220 1870 1341 0.817 1193 677 1169 172 0
Hs6-1-17-1 0.204228932 4210 17770 110 6159 5826 2799 1659 1738 583 83 81 0 8050 7094 3732 4555 4514 963 71 70 0 1.288 1.641 1.217 0.967 2.565 1.006 0.736 80 518 7995 6706 0.365 4500 3495 4167 2539 0
Hs6-1-18-1 null 4390 17760 100 2600 2784 1214 1605 1764 1093 46 20 0 4362 3928 2105 4532 4512 1566 15 1 0 -5.853 -1.952 1.538 0.972 4.162 0.601 0.393 80 466 825 575 Error 995 -170 1179 -604 -50
Hs6-1-19-1 0.203576172 4550 17770 110 6531 7630 4393 1901 2030 1160 81 75 0 9207 8904 5090 4583 4697 1685 66 58 0 1.001 1.326 1.079 0.918 2.777 1.012 0.811 80 497 9254 10050 0.002 4630 4624 5729 4321 0
Hs6-1-20-1 null 4740 17760 100 3510 4449 2643 2091 2155 766 68 48 0 5181 5521 3074 4664 4732 1294 32 25 0 2.745 2.751 1.273 1.234 3.152 0.923 0.582 80 474 1936 3215 1.457 1419 517 2358 857 -50

Total number of rows: 20000

Table truncated, full table size 3853 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap