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Sample GSM50333 Query DataSets for GSM50333
Status Public on Jan 02, 2006
Title WTA_LCM_NOR5
Sample type RNA
 
Channel 1
Source name LCM_NOR5, 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 1950 19200 110 907 924 467 265 273 86 88 80 0 1122 1028 502 333 340 67 83 81 0 0.814 0.948 0.93 0.938 1.958 0.943 0.869 80 554 1431 1354 -0.297 642 789 659 695 0
Hs6-1-2-1 null 2130 19200 100 1180 1158 484 257 261 75 97 95 0 1180 1154 494 332 342 77 88 83 0 1.088 1.096 1.057 1.116 2.329 1.06 0.884 80 461 1771 1723 0.122 923 848 901 822 0
Hs6-1-3-1 null 2310 19190 50 405 380 80 261 262 76 66 41 0 777 761 74 347 378 127 100 100 0 0.335 0.287 0.354 0.249 2.847 0.31 0.39 12 104 574 533 -1.578 144 430 119 414 0
Hs6-1-4-1 null 2480 19200 110 821 801 351 258 268 99 85 78 0 1019 948 407 344 369 346 71 50 0 0.834 0.899 0.866 0.914 1.928 0.481 0.52 80 575 1238 1147 -0.262 563 675 543 604 0
Hs6-1-5-1 null 2660 19200 70 681 649 201 263 278 88 90 84 0 971 898 285 332 349 103 90 90 0 0.654 0.682 0.688 0.605 1.572 0.636 0.694 32 225 1057 952 -0.612 418 639 386 566 0
Hs6-1-6-1 null 2820 19200 110 1421 1303 497 260 266 76 97 96 0 1668 1540 626 340 346 61 96 93 0 0.874 0.869 0.859 0.916 1.523 0.838 0.899 80 483 2489 2243 -0.194 1161 1328 1043 1200 0
Hs6-1-7-1 0.085729 2990 19190 110 4952 4403 1990 277 318 223 100 100 0 3940 3711 1717 361 390 157 100 97 0 1.306 1.232 1.211 1.287 1.371 1.216 0.959 80 541 8254 7476 0.385 4675 3579 4126 3350 0
Hs6-1-8-1 null 3190 19190 90 1253 1175 379 351 394 178 94 86 0 1324 1306 447 408 445 157 96 84 0 0.985 0.918 0.918 0.899 2.047 0.898 0.834 52 388 1818 1722 -0.022 902 916 824 898 0
Hs6-1-9-1 -0.447674 3350 19200 110 2314 2347 1146 293 313 121 98 98 0 2748 2631 1301 370 393 114 96 95 0 0.85 0.908 0.89 0.999 1.842 0.898 0.947 80 499 4399 4315 -0.235 2021 2378 2054 2261 0
Hs6-1-10-1 null 3530 19200 110 829 812 295 275 285 88 87 83 0 1018 907 354 336 349 82 87 85 0 0.812 0.94 0.921 0.906 2.127 0.944 0.816 80 476 1236 1108 -0.3 554 682 537 571 0
Hs6-1-11-1 null 3700 19200 110 1202 1106 493 253 273 118 92 82 0 1539 1383 645 327 340 96 91 86 0 0.783 0.808 0.806 0.912 2.076 0.779 0.891 80 463 2161 1909 -0.353 949 1212 853 1056 0
Hs6-1-12-1 null 3870 19190 110 1140 1063 441 247 266 117 93 83 0 1061 959 429 336 346 94 82 76 0 1.232 1.31 1.309 1.473 1.956 1.22 0.861 80 428 1618 1439 0.301 893 725 816 623 0
Hs6-1-13-1 -0.199186 4050 19200 180 1776 1694 442 260 274 99 98 95 0 1756 1663 405 351 364 91 96 94 0 1.079 1.093 1.076 1.09 1.357 1.083 0.923 256 1153 2921 2746 0.11 1516 1405 1434 1312 0
Hs6-1-14-1 null 4220 19200 130 1658 1538 819 258 293 713 69 48 0 1569 1451 746 325 343 169 81 77 0 1.125 1.137 1.125 1.126 1.615 1.119 0.928 120 556 2644 2406 0.17 1400 1244 1280 1126 0
Hs6-1-15-1 null 4410 19190 110 1039 1067 519 256 321 996 37 0 0 1083 1085 548 319 343 294 71 56 0 1.025 1.059 1.075 1.142 2.152 2.698 0.657 80 506 1547 1577 0.035 783 764 811 766 0
Hs6-1-16-1 null 4580 19200 110 616 617 255 239 256 194 70 50 0 894 824 370 320 332 116 77 72 0 0.657 0.75 0.719 0.677 2.349 0.72 0.733 80 498 951 882 -0.606 377 574 378 504 0
Hs6-1-17-1 -0.288868 4750 19190 110 1721 1508 737 245 253 79 96 91 0 1732 1543 762 320 329 66 93 91 0 1.045 1.033 1.011 1.006 1.48 1.01 0.925 80 510 2888 2486 0.064 1476 1412 1263 1223 0
Hs6-1-18-1 null 4920 19200 100 576 579 229 223 237 79 88 77 0 781 724 301 306 309 60 82 78 0 0.743 0.852 0.827 0.775 1.815 0.807 0.767 80 396 828 774 -0.428 353 475 356 418 0
Hs6-1-19-1 -0.318301 5110 19200 190 1634 1581 426 235 244 80 98 98 0 1709 1659 419 324 334 83 97 96 0 1.01 1.008 0.99 1.018 1.422 1.004 0.922 256 1250 2784 2681 0.015 1399 1385 1346 1335 0
Hs6-1-20-1 null 5260 19200 140 1091 1174 791 234 243 79 84 80 0 1072 1148 718 317 329 95 76 72 0 1.135 1.131 1.099 1.153 2.431 1.089 0.926 156 617 1612 1771 0.183 857 755 940 831 0

Total number of rows: 20000

Table truncated, full table size 3574 Kbytes.




Supplementary data files not provided
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