NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM50334 Query DataSets for GSM50334
Status Public on Jan 02, 2006
Title WTA_LCM_PCA1
Sample type RNA
 
Channel 1
Source name LCM_PCA1, 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 1500 18190 110 1175 1185 294 125 139 214 100 100 0 944 927 138 102 105 23 100 100 0 1.247 1.285 1.274 1.253 1.265 1.624 0.703 80 555 1892 1885 0.318 1050 842 1060 825 0
Hs6-1-2-1 null 1680 18200 110 1531 1574 391 127 130 41 100 100 0 1334 1327 221 102 104 23 100 100 0 1.14 1.181 1.175 1.164 1.251 1.22 0.91 80 491 2636 2672 0.189 1404 1232 1447 1225 0
Hs6-1-3-1 null 1850 18180 90 171 179 50 124 130 41 55 30 0 234 225 49 105 106 24 94 90 0 0.364 0.458 0.464 0.403 2.894 0.421 0.14 52 364 176 175 -1.457 47 129 55 120 0
Hs6-1-4-1 null 2020 18190 110 672 657 148 124 129 40 100 100 0 788 762 152 105 107 24 100 100 0 0.802 0.811 0.797 0.805 1.385 0.817 0.855 80 511 1231 1190 -0.318 548 683 533 657 0
Hs6-1-5-1 null 2200 18200 100 394 408 110 129 135 42 100 100 0 465 468 69 108 111 27 100 100 0 0.742 0.775 0.716 0.732 1.504 0.817 0.741 80 440 622 639 -0.43 265 357 279 360 0
Hs6-1-6-1 null 2370 18200 110 1481 1466 287 127 132 40 100 100 0 1833 1779 305 111 114 25 100 100 0 0.786 0.803 0.799 0.798 1.207 0.789 0.933 80 442 3076 3007 -0.347 1354 1722 1339 1668 0
Hs6-1-7-1 -0.668673 2540 18200 120 5149 5142 1639 126 132 43 100 100 0 5722 5464 1916 112 114 26 100 100 0 0.895 0.937 0.927 0.983 1.436 0.921 0.952 120 487 10633 10368 -0.159 5023 5610 5016 5352 0
Hs6-1-8-1 null 2720 18190 150 490 1619 7671 126 697 5159 3 3 1 751 1867 8127 113 691 5043 2 1 0 0.571 0.851 0.615 0.725 2.03 1.006 0.96 156 667 1002 3247 -0.81 364 638 1493 1754 0
Hs6-1-9-1 -0.915451 2890 18200 120 1912 1868 678 129 929 6100 0 0 0 2561 2414 936 111 934 5963 0 0 0 0.728 0.755 0.729 0.759 1.421 1.061 0.932 120 475 4233 4042 -0.458 1783 2450 1739 2303 0
Hs6-1-10-1 null 3060 18200 120 491 466 156 128 132 45 95 92 0 538 518 168 106 108 26 99 97 0 0.84 0.82 0.797 0.808 1.991 0.83 0.813 120 495 795 750 -0.251 363 432 338 412 0
Hs6-1-11-1 null 3240 18200 120 866 895 418 130 135 48 99 96 0 1434 1360 521 106 110 32 100 100 0 0.554 0.61 0.581 0.593 1.649 0.611 0.744 120 529 2064 2019 -0.851 736 1328 765 1254 0
Hs6-1-12-1 null 3410 18200 110 552 538 178 128 135 50 98 95 0 736 726 190 105 109 25 100 100 0 0.672 0.66 0.648 0.602 1.701 0.705 0.826 80 456 1055 1031 -0.574 424 631 410 621 0
Hs6-1-13-1 -0.501973 3590 18200 120 2208 2070 613 125 130 41 100 99 0 2238 2099 686 107 109 25 100 100 0 0.977 0.976 0.971 0.98 1.359 0.961 0.946 120 570 4214 3937 -0.033 2083 2131 1945 1992 0
Hs6-1-14-1 -0.40584 3760 18200 110 2067 2041 582 121 142 269 100 100 0 2081 1992 444 105 109 46 100 100 0 0.985 1.017 1.039 0.993 1.228 1.042 0.943 80 458 3922 3807 -0.022 1946 1976 1920 1887 0
Hs6-1-15-1 null 3940 18210 120 1000 1006 403 120 125 38 100 100 0 1133 1070 465 104 105 23 100 99 0 0.855 0.917 0.92 0.978 1.584 0.899 0.916 120 530 1909 1852 -0.226 880 1029 886 966 0
Hs6-1-16-1 null 4110 18200 110 740 714 178 124 126 39 100 100 0 754 730 147 102 103 22 100 100 0 0.945 0.939 0.943 0.914 1.37 0.973 0.878 80 471 1268 1218 -0.082 616 652 590 628 0
Hs6-1-17-1 -0.360358 4290 18200 110 2594 2498 759 126 129 50 100 100 0 2256 2257 543 106 108 26 100 100 0 1.148 1.103 1.075 1.077 1.284 1.14 0.931 80 510 4618 4523 0.199 2468 2150 2372 2151 0
Hs6-1-18-1 null 4460 18200 110 455 465 112 124 135 128 97 78 0 559 543 112 103 117 151 98 87 0 0.726 0.775 0.736 0.753 1.398 0.784 0.755 80 477 787 781 -0.462 331 456 341 440 0
Hs6-1-19-1 -0.753559 4630 18200 110 2421 2350 460 124 132 61 100 100 0 2681 2688 522 108 116 56 100 100 0 0.893 0.863 0.823 0.861 1.198 0.906 0.923 80 496 4870 4806 -0.164 2297 2573 2226 2580 0
Hs6-1-20-1 null 4810 18200 110 1239 1250 252 126 132 59 100 100 0 1450 1518 287 103 111 55 100 100 0 0.826 0.794 0.786 0.79 1.205 0.799 0.923 80 497 2460 2539 -0.275 1113 1347 1124 1415 0

Total number of rows: 20000

Table truncated, full table size 3604 Kbytes.




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