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Sample GSM50349 Query DataSets for GSM50349
Status Public on Jan 02, 2006
Title Tissue_WTA300ng1
Sample type RNA
 
Channel 1
Source name PCA1, localized prostate adenocarcinoma tissue sample, 300ng RNA WTA one PCR, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, Commercially available pool of benign prostate tissue total RNA, 300ng RNA WTA one PCR, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See 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 GPL2012
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
Hs3-1-1-1 -0.98769 2090 17550 110 2082 2137 1110 208 229 106 100 98 0 3080 3199 1612 603 627 252 88 85 0 0.757 0.743 0.703 0.775 3.021 0.63 0.53 80 568 4351 4525 -0.402 1874 2477 1929 2596 0
Hs3-1-2-1 -0.430374 2270 17550 110 5048 5720 3480 206 232 126 100 100 0 5382 5579 3264 570 597 291 95 90 0 1.006 1.101 1.117 1.141 3.211 1.121 0.534 80 462 9654 10523 0.009 4842 4812 5514 5009 0
Hs3-1-3-1 null 2430 17550 100 317 330 141 181 200 121 52 28 0 715 773 318 496 497 234 47 31 0 0.621 0.538 0.409 0.429 3.08 0.248 0.203 80 456 355 426 -0.687 136 219 149 277 -50
Hs3-1-4-1 null 2600 17530 70 1776 1699 1098 167 207 213 87 78 0 2200 2592 1792 451 528 541 81 59 0 0.92 0.716 0.764 0.758 7.402 0.306 0.115 32 236 3358 3673 -0.12 1609 1749 1532 2141 0
Hs3-1-5-1 null 2780 17560 100 107 215 332 140 168 159 11 10 0 189 571 1116 306 422 434 13 7 0 0.282 0.283 0.388 0.403 3.355 0.096 0.083 80 483 -150 340 -1.826 -33 -117 75 265 -50
Hs3-1-6-1 null 2950 17580 60 623 790 469 163 178 102 93 81 0 1270 1307 906 346 426 332 65 56 0 0.498 0.652 0.345 0.437 4.243 0.235 0.089 32 176 1384 1588 -1.006 460 924 627 961 0
Hs3-1-7-1 -1.12236 3130 17560 120 9983 11726 8467 184 191 80 100 100 0 13587 15541 11934 510 478 138 96 95 0 0.749 0.768 0.73 0.9 4.463 0.681 0.61 120 613 22876 26573 -0.416 9799 13077 11542 15031 0
Hs3-1-8-1 -0.630577 3300 17550 110 2104 2540 1224 199 206 66 100 100 0 2877 2975 1692 541 545 67 96 92 0 0.815 0.962 0.897 1.191 2.976 0.818 0.558 80 534 4241 4775 -0.294 1905 2336 2341 2434 0
Hs3-1-9-1 0.231339 3480 17550 90 2410 2644 1161 201 208 68 100 100 0 2056 2343 1310 555 561 72 94 90 0 1.472 1.366 1.598 1.82 2.981 1.178 0.489 52 400 3710 4231 0.557 2209 1501 2443 1788 0
Hs3-1-10-1 null 3660 17560 90 767 764 285 192 200 60 98 88 0 1408 1342 489 550 554 66 92 88 0 0.67 0.722 0.62 0.696 3.611 0.488 0.32 52 379 1433 1364 -0.577 575 858 572 792 0
Hs3-1-11-1 -1.240111 3830 17560 100 3218 3079 1477 204 284 400 100 93 0 5156 4722 2302 562 594 224 98 95 0 0.656 0.691 0.63 0.802 3.201 0.582 0.491 80 496 7608 7035 -0.608 3014 4594 2875 4160 0
Hs3-1-12-1 -1.187142 4030 17560 50 3008 2790 702 1065 1665 1399 66 0 0 3451 3257 1112 861 1818 1613 75 25 0 0.75 0.72 0.616 0.735 2.741 0.779 0.23 12 104 4533 4121 -0.415 1943 2590 1725 2396 0
Hs3-1-13-1 null 4180 17570 100 4420 4510 1282 3575 3117 2219 18 0 0 5021 4756 1480 3981 3311 2435 7 0 0 0.813 1.206 0.868 0.633 2.806 1.106 0.31 80 459 1885 1710 -0.3 845 1040 935 775 -50
Hs3-1-14-1 null 4360 17570 100 572 1577 1923 242 1313 2212 22 10 0 669 1485 1621 579 1689 2269 17 5 0 3.667 1.474 0.997 1.61 6.963 0.985 0.685 80 462 420 2241 1.874 330 90 1335 906 -50
Hs3-1-15-1 null 4530 17580 110 1740 1740 859 214 220 71 100 97 0 2207 2246 978 568 571 66 96 96 0 0.931 0.909 0.769 0.858 2.89 0.863 0.523 80 477 3165 3204 -0.103 1526 1639 1526 1678 0
Hs3-1-16-1 null 4710 17570 110 1508 1501 528 211 218 66 100 100 0 1953 1954 829 553 559 72 93 91 0 0.926 0.921 0.829 1.041 2.667 0.763 0.52 80 498 2697 2691 -0.11 1297 1400 1290 1401 0
Hs3-1-17-1 0.08295 4880 17570 110 15469 15827 7574 211 255 211 100 100 0 9617 9710 5692 517 539 226 98 95 0 1.677 1.699 1.69 2.326 3.91 1.753 0.572 80 534 24358 24809 0.746 15258 9100 15616 9193 0
Hs3-1-18-1 0.140408 5060 17570 90 7960 7458 2828 259 848 1206 98 94 0 4701 4614 1924 525 862 802 94 86 0 1.844 1.761 1.681 1.878 2.6 1.98 0.424 52 306 11877 11288 0.883 7701 4176 7199 4089 0
Hs3-1-19-1 -0.670814 5230 17570 210 9229 9222 1999 236 560 912 100 99 0 9419 9447 2580 560 875 1073 98 97 0 1.015 1.011 0.982 1.061 1.675 0.967 0.713 316 1559 17852 17873 0.022 8993 8859 8986 8887 0
Hs3-1-20-1 null 5410 17570 100 696 777 331 226 321 541 41 10 0 850 905 393 569 814 1462 2 0 0 1.673 1.64 1.669 1.828 2.93 0.811 0.717 80 380 751 887 0.742 470 281 551 336 -50

Total number of rows: 20000

Table truncated, full table size 3687 Kbytes.




Supplementary data files not provided
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