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Sample GSM50303 Query DataSets for GSM50303
Status Public on Jan 02, 2006
Title WTA_LCM_NOR1
Sample type RNA
 
Channel 1
Source name LCM_NOR1, Benign 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 1460 18120 110 609 610 115 119 122 35 100 100 0 742 698 161 118 120 22 100 100 0 0.785 0.847 0.836 0.867 1.315 0.815 0.888 80 526 1114 1071 -0.349 490 624 491 580 0
Hs6-1-2-1 null 1630 18120 110 877 868 165 116 121 39 100 100 0 1005 979 249 117 120 30 100 100 0 0.857 0.872 0.853 0.896 1.347 0.846 0.903 80 482 1649 1614 -0.223 761 888 752 862 0
Hs6-1-3-1 null 1790 18110 60 123 124 35 125 127 41 12 3 0 215 211 45 125 136 44 81 50 0 -0.022 -0.012 0.42 0.465 3.023 0.264 0.033 32 176 88 85 Error -2 90 -1 86 0
Hs6-1-4-1 null 1980 18110 110 432 442 114 116 119 34 100 100 0 664 625 148 116 118 27 100 100 0 0.577 0.64 0.619 0.642 1.546 0.636 0.799 80 542 864 835 -0.794 316 548 326 509 0
Hs6-1-5-1 null 2160 18120 100 281 287 75 118 120 36 98 93 0 378 367 87 117 117 22 98 97 0 0.625 0.676 0.615 0.672 1.788 0.667 0.591 80 406 424 419 -0.679 163 261 169 250 0
Hs6-1-6-1 null 2330 18110 100 957 979 201 120 126 41 100 100 0 1393 1343 256 116 117 24 100 100 0 0.655 0.7 0.67 0.7 1.345 0.712 0.85 80 409 2114 2086 -0.609 837 1277 859 1227 0
Hs6-1-7-1 -0.255062 2500 18100 110 5081 5068 846 125 143 129 100 100 0 5206 5056 923 121 130 68 100 100 0 0.975 1.002 0.98 1.007 1.195 1.016 0.947 80 478 10041 9878 -0.037 4956 5085 4943 4935 0
Hs6-1-8-1 null 2670 18100 110 578 617 181 124 142 130 98 98 0 726 723 197 117 129 71 100 100 0 0.745 0.814 0.759 0.816 1.399 0.921 0.808 80 497 1063 1099 -0.424 454 609 493 606 0
Hs6-1-9-1 -1.120283 2850 18100 110 1412 1436 397 123 130 51 100 100 0 2409 2287 514 116 123 41 100 100 0 0.562 0.605 0.566 0.601 1.363 0.594 0.869 80 497 3582 3484 -0.831 1289 2293 1313 2171 0
Hs6-1-10-1 null 3020 18100 110 489 502 101 119 127 47 100 100 0 494 500 81 119 123 36 100 100 0 0.987 1.005 1.016 0.996 1.33 1.107 0.797 80 456 745 764 -0.019 370 375 383 381 0
Hs6-1-11-1 null 3200 18100 120 933 948 309 115 121 42 99 98 0 1297 1226 430 121 123 29 100 99 0 0.696 0.754 0.759 0.746 1.542 0.736 0.923 120 516 1994 1938 -0.524 818 1176 833 1105 0
Hs6-1-12-1 null 3380 18100 120 494 511 163 117 121 36 99 98 0 572 560 181 119 120 25 100 98 0 0.832 0.893 0.878 0.904 1.722 0.874 0.761 120 478 830 835 -0.265 377 453 394 441 0
Hs6-1-13-1 -0.563627 3550 18100 120 1729 1747 338 124 128 45 100 100 0 2218 2026 516 119 123 30 100 100 0 0.765 0.851 0.831 0.874 1.327 0.822 0.909 120 482 3704 3530 -0.387 1605 2099 1623 1907 0
Hs6-1-14-1 -0.821111 3730 18100 120 1210 1212 491 124 128 44 99 97 0 1629 1567 652 118 122 29 100 100 0 0.719 0.751 0.716 0.76 1.521 0.738 0.903 120 511 2597 2537 -0.476 1086 1511 1088 1449 0
Hs6-1-15-1 null 3900 18090 110 1245 1290 529 120 124 36 100 100 0 1195 1211 297 116 120 28 100 100 0 1.043 1.068 1.031 1.038 1.301 1.154 0.88 80 476 2204 2265 0.06 1125 1079 1170 1095 0
Hs6-1-16-1 null 4080 18090 110 433 434 116 117 121 36 100 98 0 600 572 140 117 117 22 100 100 0 0.654 0.697 0.678 0.686 1.731 0.681 0.751 80 496 799 772 -0.612 316 483 317 455 0
Hs6-1-17-1 -0.608984 4250 18090 110 1612 1667 394 120 128 56 100 100 0 2047 1916 506 121 125 35 100 100 0 0.775 0.862 0.809 0.881 1.345 0.834 0.886 80 462 3418 3342 -0.368 1492 1926 1547 1795 0
Hs6-1-18-1 null 4420 18090 100 399 411 99 118 126 59 100 98 0 575 523 143 117 123 34 100 98 0 0.614 0.722 0.688 0.755 1.652 0.688 0.759 80 421 739 699 -0.705 281 458 293 406 0
Hs6-1-19-1 -0.798487 4600 18080 110 1692 1686 425 120 125 46 100 100 0 2501 2343 684 119 124 41 100 100 0 0.66 0.704 0.704 0.716 1.336 0.704 0.893 80 471 3954 3790 -0.6 1572 2382 1566 2224 0
Hs6-1-20-1 null 4770 18090 120 971 1041 380 119 124 44 100 99 0 1155 1124 430 119 124 40 97 97 0 0.822 0.917 0.899 0.978 1.662 0.905 0.907 120 520 1888 1927 -0.282 852 1036 922 1005 0

Total number of rows: 20000

Table truncated, full table size 3570 Kbytes.




Supplementary data files not provided
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