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Sample GSM50352 Query DataSets for GSM50352
Status Public on Jan 02, 2006
Title OneRound_PCR
Sample type RNA
 
Channel 1
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA one PCR
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA one PCR
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 1670 18790 110 1837 1943 1011 273 285 101 96 92 0 2250 2367 1193 429 443 108 92 91 0 0.859 0.862 0.845 0.905 1.656 0.852 0.952 80 555 3385 3608 -0.219 1564 1821 1670 1938 0
Hs6-1-2-1 null 1850 18800 110 2418 2524 1215 234 254 97 100 98 0 2868 3155 1605 391 405 96 95 92 0 0.882 0.829 0.849 0.868 1.335 0.805 0.967 80 478 4661 5054 -0.182 2184 2477 2290 2764 0
Hs6-1-3-1 null 2010 18800 80 410 410 122 229 241 89 75 50 0 1034 1021 312 374 384 81 94 90 0 0.274 0.28 0.315 0.281 2.368 0.26 0.486 52 298 841 828 -1.866 181 660 181 647 0
Hs6-1-4-1 null 2190 18790 110 2059 2136 974 257 270 109 97 93 0 2635 2638 1164 396 420 108 95 95 0 0.805 0.838 0.835 0.838 1.241 0.838 0.967 80 536 4041 4121 -0.313 1802 2239 1879 2242 0
Hs6-1-5-1 null 2350 18800 80 988 982 367 241 265 114 96 92 0 1599 1581 589 388 412 110 96 94 0 0.617 0.621 0.613 0.632 1.503 0.598 0.889 52 295 1958 1934 -0.697 747 1211 741 1193 0
Hs6-1-6-1 -0.006070004 2540 18790 110 3622 4208 2047 306 349 172 98 97 0 4050 4345 2053 431 497 182 98 97 0 0.916 0.997 0.998 1.006 1.181 1 0.982 80 522 6935 7816 -0.126 3316 3619 3902 3914 0
Hs6-1-7-1 0.112197432 2730 18800 120 15138 17675 11364 351 461 300 100 100 0 14139 16488 10490 493 606 330 100 100 0 1.084 1.083 1.076 1.082 1.095 1.082 0.996 120 560 28433 33319 0.116 14787 13646 17324 15995 0
Hs6-1-8-1 -0.157247063 2900 18810 110 3218 3174 1321 307 416 261 98 96 0 3604 3619 1471 430 558 271 98 96 0 0.917 0.899 0.882 0.9 1.177 0.895 0.972 80 450 6085 6056 -0.125 2911 3174 2867 3189 0
Hs6-1-9-1 0.015500912 3070 18800 110 11535 12188 7579 328 415 242 100 100 0 12079 12235 7151 443 552 246 100 100 0 0.963 1.006 0.983 0.97 1.161 1.025 0.99 80 511 22843 23652 -0.054 11207 11636 11860 11792 0
Hs6-1-10-1 null 3250 18810 110 1403 1367 582 293 342 173 92 86 0 1908 1862 783 413 472 173 93 88 0 0.742 0.741 0.779 0.772 1.563 0.747 0.911 80 485 2605 2523 -0.43 1110 1495 1074 1449 0
Hs6-1-11-1 -0.043495393 3410 18800 110 5040 4817 2278 294 337 162 98 97 0 4963 5059 2260 418 473 169 98 98 0 1.044 0.975 0.974 0.963 1.204 0.984 0.984 80 479 9291 9164 0.062 4746 4545 4523 4641 0
Hs6-1-12-1 null 3590 18810 110 1914 2055 962 313 350 171 97 93 0 2302 2435 1109 415 475 173 95 95 0 0.848 0.862 0.881 0.874 1.361 0.867 0.957 80 397 3488 3762 -0.237 1601 1887 1742 2020 0
Hs6-1-13-1 0.046156102 3780 18810 200 12279 10943 3413 424 453 231 99 99 0 11820 10615 3233 591 611 254 99 99 0 1.056 1.049 1.049 1.051 1.15 1.047 0.99 316 1394 23084 20543 0.078 11855 11229 10519 10024 0
Hs6-1-14-1 null 3950 18800 100 300 425 322 407 417 183 18 15 0 400 555 383 547 567 200 18 11 0 0.728 2.25 0.825 0.762 2.988 1.004 0.703 80 349 -254 26 -0.458 -107 -147 18 8 -50
Hs6-1-15-1 0.010193366 4120 18810 110 3537 3967 2130 350 381 173 100 97 0 3753 4036 2096 489 518 180 95 95 0 0.976 1.02 1.028 1.09 1.59 1.016 0.98 80 463 6451 7164 -0.034 3187 3264 3617 3547 0
Hs6-1-16-1 null 4290 18810 110 1334 1261 480 282 314 141 97 92 0 1775 1851 726 407 452 148 95 93 0 0.769 0.678 0.664 0.705 1.401 0.675 0.903 80 482 2420 2423 -0.379 1052 1368 979 1444 0
Hs6-1-17-1 -0.007822154 4460 18810 110 6611 6155 2537 275 297 123 100 100 0 6495 6309 2607 400 439 135 100 100 0 1.04 0.995 0.997 0.997 1.127 0.987 0.988 80 497 12431 11789 0.056 6336 6095 5880 5909 0
Hs6-1-18-1 null 4630 18820 90 1802 1618 529 265 281 114 100 100 0 2145 2066 750 367 395 111 98 98 0 0.864 0.796 0.767 0.833 1.469 0.779 0.932 52 310 3315 3052 -0.21 1537 1778 1353 1699 0
Hs6-1-19-1 0.131730995 4820 18810 190 13899 12870 3434 473 598 404 100 100 0 12735 11878 2994 638 764 476 100 99 0 1.11 1.103 1.103 1.09 1.124 1.108 0.991 256 1377 25523 23637 0.15 13426 12097 12397 11240 0
Hs6-1-20-1 null 4990 18810 100 1121 1754 1603 474 613 396 57 41 0 1144 1929 1772 616 756 416 55 38 0 1.225 0.975 1.045 1.188 2.343 1.005 0.959 80 395 1175 2593 0.293 647 528 1280 1313 -50

Total number of rows: 20000

Table truncated, full table size 3790 Kbytes.




Supplementary data files not provided
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