NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM50357 Query DataSets for GSM50357
Status Public on Jan 02, 2006
Title Round2_PCR_from_Round1
Sample type RNA
 
Channel 1
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA two PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name prostate tissue total RNA, 25ng WTA two 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 -0.050339587 1630 17730 110 2257 2149 757 169 175 61 100 100 0 2619 2462 817 254 261 50 100 100 0 0.883 0.897 0.898 0.9 1.248 0.896 0.955 80 538 4453 4188 -0.18 2088 2365 1980 2208 0
Hs6-1-2-1 -0.23099582 1800 17730 100 2398 2339 932 174 178 61 100 100 0 3145 3043 1108 251 256 46 100 100 0 0.768 0.775 0.762 0.769 1.252 0.789 0.952 80 421 5118 4957 -0.38 2224 2894 2165 2792 0
Hs6-1-3-1 null 1970 17730 80 242 257 106 175 180 63 50 30 0 832 742 221 252 255 46 92 92 0 0.116 0.167 0.176 0.178 3.553 0.196 0.251 52 298 647 572 -3.114 67 580 82 490 0
Hs6-1-4-1 null 2140 17730 100 2052 1920 681 206 253 247 96 92 0 2473 2373 803 280 407 420 96 88 0 0.842 0.819 0.807 0.8 1.287 0.806 0.93 80 426 4039 3807 -0.249 1846 2193 1714 2093 0
Hs6-1-5-1 null 2310 17740 100 917 903 268 222 274 259 92 76 0 1623 1578 536 327 465 438 90 82 0 0.536 0.544 0.555 0.578 1.517 0.509 0.84 80 394 1991 1932 -0.899 695 1296 681 1251 0
Hs6-1-6-1 0.116316032 2480 17740 110 3850 3356 1963 177 182 65 95 93 0 3890 3440 1999 248 252 55 91 88 0 1.009 0.996 1.002 1.039 2.061 0.982 0.962 80 460 7315 6371 0.012 3673 3642 3179 3192 0
Hs6-1-7-1 0.178749098 2660 17740 120 20159 17334 7509 175 184 68 100 100 0 19856 16889 7496 250 253 53 100 100 0 1.019 1.031 1.033 1.075 1.336 1.025 0.983 120 518 39590 33798 0.028 19984 19606 17159 16639 0
Hs6-1-8-1 -0.142715689 2840 17740 120 1947 1927 947 173 181 62 100 99 0 2216 2310 1137 252 255 52 100 98 0 0.903 0.852 0.883 0.879 1.346 0.843 0.944 120 508 3738 3812 -0.147 1774 1964 1754 2058 0
Hs6-1-9-1 0.078528004 3020 17740 120 6934 7301 4412 171 182 65 100 100 0 7573 7666 4712 250 252 51 100 100 0 0.924 0.961 0.975 0.984 1.274 0.952 0.979 120 520 14086 14546 -0.115 6763 7323 7130 7416 0
Hs6-1-10-1 null 3190 17740 120 1040 1055 440 178 184 61 100 97 0 1470 1425 628 249 252 50 100 97 0 0.706 0.746 0.768 0.768 1.535 0.73 0.905 120 521 2083 2053 -0.502 862 1221 877 1176 0
Hs6-1-11-1 -0.018589026 3370 17740 120 3462 3489 1962 177 183 63 100 100 0 3814 3934 2126 252 257 52 100 100 0 0.922 0.9 0.911 0.888 1.276 0.907 0.974 120 540 6847 6994 -0.117 3285 3562 3312 3682 0
Hs6-1-12-1 null 3540 17740 110 1660 1579 672 172 179 62 98 96 0 2144 2076 810 252 256 50 98 98 0 0.786 0.771 0.786 0.757 1.384 0.786 0.934 80 490 3380 3231 -0.347 1488 1892 1407 1824 0
Hs6-1-13-1 0.001790611 3720 17740 110 5392 4429 2418 176 184 63 100 100 0 5476 5031 2609 252 257 49 98 97 0 0.998 0.89 0.918 0.938 1.565 0.901 0.974 80 511 10440 9032 -0.002 5216 5224 4253 4779 0
Hs6-1-14-1 0.064336613 3890 17750 100 4674 4731 2359 179 185 62 100 100 0 5327 5029 2450 251 253 54 100 100 0 0.886 0.953 0.959 0.976 1.343 0.954 0.965 80 422 9571 9330 -0.175 4495 5076 4552 4778 0
Hs6-1-15-1 0.066491784 4070 17750 120 4151 3757 1678 180 187 64 100 100 0 4561 4003 1736 251 255 59 100 99 0 0.921 0.953 0.962 0.941 1.284 0.955 0.973 120 541 8281 7329 -0.118 3971 4310 3577 3752 0
Hs6-1-16-1 null 4240 17750 100 1191 1120 529 180 188 65 97 90 0 1657 1576 701 254 258 48 96 96 0 0.721 0.711 0.682 0.685 1.456 0.712 0.905 80 432 2414 2262 -0.473 1011 1403 940 1322 0
Hs6-1-17-1 0.055538717 4420 17750 100 5875 5131 2367 176 183 64 100 100 0 6024 5485 2263 253 257 51 100 98 0 0.988 0.947 0.949 0.926 1.317 0.969 0.975 80 440 11470 10187 -0.018 5699 5771 4955 5232 0
Hs6-1-18-1 null 4590 17750 100 1172 1088 460 180 187 62 96 95 0 1725 1582 633 256 259 52 96 96 0 0.675 0.685 0.688 0.642 1.54 0.69 0.922 80 418 2461 2234 -0.566 992 1469 908 1326 0
Hs6-1-19-1 0.130522728 4770 17760 120 5365 6085 3415 183 193 69 100 100 0 5095 6174 3638 259 262 54 100 99 0 1.072 0.998 1.006 1.051 1.347 0.977 0.974 120 525 10018 11817 0.1 5182 4836 5902 5915 0
Hs6-1-20-1 -0.054220391 4950 17760 120 2298 2652 1589 184 190 65 100 100 0 2538 3065 1807 253 258 52 100 100 0 0.925 0.878 0.88 0.879 1.383 0.877 0.956 120 502 4399 5280 -0.112 2114 2285 2468 2812 0

Total number of rows: 20000

Table truncated, full table size 3755 Kbytes.




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