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Sample GSM50311 Query DataSets for GSM50311
Status Public on Jan 02, 2006
Title WTA_LCM_NOR3
Sample type RNA
 
Channel 1
Source name LCM_NOR3, 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 1290 18660 100 957 1070 582 277 292 108 86 77 0 1295 1201 725 215 221 60 82 77 0 0.63 0.804 0.836 0.865 2.296 0.798 0.88 80 506 1760 1779 -0.667 680 1080 793 986 0
Hs6-1-2-1 null 1470 18650 90 1670 1501 752 284 296 106 88 84 0 1752 1523 754 214 224 72 94 90 0 0.901 0.93 0.903 0.822 2.128 0.942 0.924 52 383 2924 2526 -0.15 1386 1538 1217 1309 0
Hs6-1-3-1 null 1640 18650 50 423 417 92 274 302 103 66 25 0 572 577 94 222 232 97 100 91 0 0.426 0.403 0.415 0.301 3.406 0.404 0.25 12 104 499 498 -1.232 149 350 143 355 0
Hs6-1-4-1 null 1820 18660 110 899 907 463 295 306 99 85 75 0 925 1014 619 230 239 68 82 80 0 0.869 0.781 0.78 0.796 2.272 0.77 0.833 80 560 1299 1396 -0.202 604 695 612 784 0
Hs6-1-5-1 null 1990 18650 60 638 650 212 294 308 104 87 71 0 904 829 268 220 236 87 93 90 0 0.503 0.585 0.58 0.534 1.688 0.62 0.646 32 176 1028 965 -0.992 344 684 356 609 0
Hs6-1-6-1 null 2150 18650 100 1421 1388 620 296 387 1200 43 1 0 2112 2049 1036 234 279 584 81 71 0 0.599 0.602 0.574 0.648 1.747 0.582 0.903 80 462 3003 2907 -0.739 1125 1878 1092 1815 0
Hs6-1-7-1 -0.043613 2340 18650 110 7170 7387 3930 314 329 122 100 100 0 10224 9750 5276 243 259 91 100 100 0 0.687 0.744 0.762 0.76 1.208 0.746 0.976 80 502 16837 16580 -0.542 6856 9981 7073 9507 0
Hs6-1-8-1 null 2510 18650 120 1068 1189 596 335 353 138 90 85 0 1230 1320 724 258 282 106 94 85 0 0.754 0.804 0.803 0.839 1.727 0.818 0.891 120 547 1705 1916 -0.407 733 972 854 1062 0
Hs6-1-9-1 -0.525866 2680 18650 120 2067 2524 1758 338 355 131 98 93 0 2729 3446 2498 262 287 101 97 96 0 0.701 0.687 0.696 0.724 1.684 0.691 0.957 120 551 4196 5370 -0.513 1729 2467 2186 3184 0
Hs6-1-10-1 null 2870 18650 120 997 1014 377 337 357 129 95 88 0 853 915 395 255 278 99 95 85 0 1.104 1.026 1.067 1.17 2.073 1.023 0.804 120 527 1258 1337 0.142 660 598 677 660 0
Hs6-1-11-1 null 3040 18650 120 1733 1864 1032 327 341 120 96 95 0 1847 1993 1145 232 257 92 99 95 0 0.871 0.873 0.914 0.875 1.467 0.886 0.933 120 510 3021 3298 -0.2 1406 1615 1537 1761 0
Hs6-1-12-1 null 3210 18650 110 1161 1185 478 308 316 109 97 90 0 1436 1324 591 229 240 78 97 96 0 0.707 0.801 0.851 0.814 1.563 0.807 0.863 80 336 2060 1972 -0.501 853 1207 877 1095 0
Hs6-1-13-1 0.273389 3390 18650 230 3671 3432 1298 352 366 136 94 94 0 3236 3009 1210 300 329 139 94 93 0 1.13 1.137 1.139 1.164 1.466 1.121 0.963 392 2039 6255 5789 0.177 3319 2936 3080 2709 0
Hs6-1-14-1 null 3570 18640 90 438 623 433 317 327 113 51 40 0 291 655 617 231 243 71 48 44 0 2.017 0.722 0.832 1.198 2.613 0.728 0.796 52 268 181 730 1.012 121 60 306 424 -50
Hs6-1-15-1 null 3740 18640 120 1122 1333 716 338 349 125 95 90 0 1312 1497 904 265 277 89 95 92 0 0.749 0.808 0.853 0.851 1.644 0.8 0.91 120 531 1831 2227 -0.417 784 1047 995 1232 0
Hs6-1-16-1 null 3900 18640 100 1040 1073 432 326 336 116 92 91 0 1333 1184 534 230 245 74 95 88 0 0.647 0.783 0.763 0.84 1.787 0.783 0.849 80 406 1817 1701 -0.627 714 1103 747 954 0
Hs6-1-17-1 -0.444187 4080 18630 110 2111 2287 1030 323 332 110 98 97 0 2909 2866 1247 223 237 70 100 100 0 0.666 0.743 0.732 0.716 1.43 0.756 0.935 80 536 4474 4607 -0.587 1788 2686 1964 2643 0
Hs6-1-18-1 null 4270 18640 100 789 782 305 304 311 103 86 77 0 998 891 411 215 229 74 91 87 0 0.619 0.707 0.707 0.709 1.807 0.821 0.808 80 359 1268 1154 -0.691 485 783 478 676 0
Hs6-1-19-1 -0.173176 4440 18630 210 2884 2851 650 333 348 131 100 99 0 3269 3168 664 289 313 156 100 99 0 0.856 0.875 0.858 0.874 1.22 0.875 0.942 316 1793 5531 5397 -0.224 2551 2980 2518 2879 0
Hs6-1-20-1 null 4620 18630 90 337 360 113 314 326 115 25 5 0 295 292 95 247 267 88 21 7 0 0.479 1.022 1.307 1.473 3.591 2.158 0.097 52 304 71 91 -1.061 23 48 46 45 -50

Total number of rows: 20000

Table truncated, full table size 3638 Kbytes.




Supplementary data files not provided

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