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Sample GSM50355 Query DataSets for GSM50355
Status Public on Jan 02, 2006
Title FourRound_PCR
Sample type RNA
 
Channel 1
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA four PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, commercially available pooled benign prostate tissue total RNA, 25ng WTA four 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 1500 17770 70 3870 4137 1746 1387 1610 833 87 75 0 8374 7700 2776 5795 6009 1660 68 37 0 0.963 1.444 1.034 0.817 2.943 0.534 0.491 32 216 5062 4655 -0.055 2483 2579 2750 1905 0
Hs6-1-2-1 0.275472309 1640 17770 110 6021 5519 3010 1192 1274 502 83 81 0 8771 8166 4436 6762 7077 1704 51 37 0 2.404 3.082 1.316 0.828 7.236 0.925 0.492 80 488 6838 5731 1.265 4829 2009 4327 1404 0
Hs6-1-3-1 null 1830 17760 100 1237 1369 557 1253 1310 489 20 7 0 5311 4674 1967 7740 7412 1663 0 0 0 0.007 -0.038 0.063 0.053 4.057 0.036 0.016 80 482 -2445 -2950 -7.246 -16 -2429 116 -3066 -50
Hs6-1-4-1 null 2030 17770 120 4871 5184 1784 1275 1328 431 100 99 0 9299 9164 2090 7991 7718 1477 46 22 0 2.749 3.332 2.248 2.638 2.415 1.112 0.402 120 563 4904 5082 1.459 3596 1308 3909 1173 0
Hs6-1-5-1 null 2190 17760 100 2390 2449 721 1273 1312 434 86 62 0 6236 5950 1583 7689 7458 1597 0 0 0 -0.769 -0.676 4.527 2.149 4.828 0.134 0.018 80 330 -336 -563 Error 1117 -1453 1176 -1739 -50
Hs6-1-6-1 0.213581848 2340 17780 120 5720 5954 2821 1265 1366 609 91 87 0 9113 8787 3769 7045 7124 1752 53 36 0 2.154 2.692 1.561 2.033 2.789 1.012 0.633 120 441 6523 6431 1.107 4455 2068 4689 1742 0
Hs6-1-7-1 0.089420442 2520 17770 130 16581 19632 13152 1258 1420 756 94 92 0 19085 21809 13174 6805 6973 1713 86 82 0 1.248 1.225 1.195 1.164 2.109 1.085 0.955 120 593 27603 33378 0.319 15323 12280 18374 15004 0
Hs6-1-8-1 null 2710 17760 100 3044 3589 1829 1266 1395 652 81 65 0 6910 6862 2529 6357 6759 1643 38 15 0 3.215 4.6 1.373 1.07 3.454 0.754 0.375 80 422 2331 2828 1.685 1778 553 2323 505 -50
Hs6-1-9-1 0.217182571 2860 17780 120 7761 8799 5107 1334 1491 787 95 92 0 10441 11418 5764 6250 6692 1691 73 54 0 1.534 1.444 1.336 1.681 2.588 1.063 0.827 120 563 10618 12633 0.617 6427 4191 7465 5168 0
Hs6-1-10-1 null 3060 17760 100 2996 3217 1429 1470 1758 1086 70 31 0 6359 6083 2434 6491 6803 1729 16 6 0 -11.561 -4.282 1.487 1.352 5.926 0.465 0.178 80 503 1394 1339 Error 1526 -132 1747 -408 -50
Hs6-1-11-1 null 3240 17770 70 5333 5466 1981 1755 2147 1240 90 75 0 8436 7978 3100 5793 6115 1445 68 46 0 1.354 1.698 1.218 1.09 3.677 0.751 0.509 32 236 6221 5896 0.437 3578 2643 3711 2185 0
Hs6-1-12-1 null 3420 17770 70 4882 5011 1417 1605 2098 1342 93 65 0 9330 8842 2811 5825 6133 1589 78 56 0 0.935 1.129 0.933 1.015 1.499 0.675 0.646 32 214 6782 6423 -0.097 3277 3505 3406 3017 0
Hs6-1-13-1 0.655817289 3570 17770 120 7489 7711 3332 1229 1336 897 95 90 0 10743 10312 4168 6893 6937 1549 68 55 0 1.626 1.896 1.501 1.722 2.359 1.16 0.737 120 558 10110 9901 0.701 6260 3850 6482 3419 0
Hs6-1-14-1 null 3740 17770 100 6591 7371 4238 1193 1215 422 95 93 0 7968 8777 4652 7484 7118 1541 43 36 0 11.153 4.778 1.706 2.356 3.827 1.271 0.477 80 447 5882 7471 3.479 5398 484 6178 1293 -50
Hs6-1-15-1 null 3950 17780 110 5044 5191 1697 1181 1272 568 98 95 0 8522 8231 2061 6954 6859 1622 47 13 0 2.464 3.14 2.19 2.306 1.68 1.134 0.371 80 494 5431 5287 1.301 3863 1568 4010 1277 0
Hs6-1-16-1 null 4120 17770 100 2664 2775 1125 1149 1280 606 82 58 0 5964 5560 2399 7007 6799 1512 8 0 0 -1.453 -1.124 2.86 1.638 6.471 0.17 0.039 80 390 472 179 Error 1515 -1043 1626 -1447 -50
Hs6-1-17-1 0.63213435 4270 17770 120 7042 7322 3237 1155 1273 591 96 95 0 10645 10339 3954 6989 6879 1457 69 55 0 1.61 1.841 1.471 1.716 1.65 1.138 0.656 120 558 9543 9517 0.687 5887 3656 6167 3350 0
Hs6-1-18-1 null 4470 17770 100 3177 3546 1838 1150 1239 582 81 71 0 6474 6325 2983 7181 6844 1509 25 7 0 -2.867 -2.799 2.075 1.637 4.752 0.535 0.217 80 456 1320 1540 Error 2027 -707 2396 -856 -50
Hs6-1-19-1 0.160888492 4660 17770 130 11635 12460 5423 1136 1230 776 100 99 0 14681 15323 5733 7235 6987 1628 86 80 0 1.41 1.4 1.343 1.531 1.507 1.115 0.888 120 593 17945 19412 0.496 10499 7446 11324 8088 0
Hs6-1-20-1 null 4820 17770 100 4219 4964 3125 1243 1452 1014 78 65 0 7774 7665 3936 6155 6437 1729 47 27 0 1.838 2.464 1.318 1.169 3.352 0.93 0.639 80 419 4595 5231 0.878 2976 1619 3721 1510 -50

Total number of rows: 20000

Table truncated, full table size 3912 Kbytes.




Supplementary data files not provided
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