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Sample GSM50336 Query DataSets for GSM50336
Status Public on Jan 02, 2006
Title WTA_LCM_PCA3
Sample type RNA
 
Channel 1
Source name LCM_PCA3, cancerous 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 2250 18660 100 4265 4164 1827 211 218 77 97 97 0 3241 2954 1200 304 310 58 96 95 0 1.38 1.492 1.505 1.471 1.243 1.509 0.975 80 496 6991 6603 0.465 4054 2937 3953 2650 0
Hs6-1-2-1 null 2420 18670 80 2505 2212 917 215 224 77 100 96 0 2668 2381 964 302 313 64 96 92 0 0.968 0.961 0.938 1.021 1.516 0.97 0.96 52 291 4656 4076 -0.047 2290 2366 1997 2079 0
Hs6-1-3-1 null 2580 18650 80 339 345 155 198 211 72 63 50 0 866 754 341 307 309 55 80 78 0 0.252 0.329 0.329 0.252 2.565 0.335 0.452 52 328 700 594 -1.987 141 559 147 447 0
Hs6-1-4-1 null 2770 18660 100 1637 1550 714 201 209 75 93 92 0 2174 2050 988 297 300 54 92 91 0 0.765 0.77 0.751 0.782 1.263 0.753 0.961 80 490 3313 3102 -0.386 1436 1877 1349 1753 0
Hs6-1-5-1 null 2940 18660 100 1037 1046 534 205 214 74 95 90 0 1187 1203 604 304 307 52 91 88 0 0.942 0.935 0.923 0.925 1.64 0.922 0.895 80 452 1715 1740 -0.086 832 883 841 899 0
Hs6-1-6-1 null 3120 18660 100 4279 3950 2165 207 215 66 96 95 0 4810 4220 2368 303 305 54 93 93 0 0.903 0.956 0.952 1.042 1.768 0.941 0.983 80 420 8579 7660 -0.146 4072 4507 3743 3917 0
Hs6-1-7-1 -0.402994 3290 18660 120 13485 13517 8004 211 217 73 100 99 0 15470 15229 9239 303 306 50 100 100 0 0.875 0.891 0.893 0.925 1.18 0.882 0.995 120 580 28441 28232 -0.192 13274 15167 13306 14926 0
Hs6-1-8-1 null 3470 18650 100 1715 1609 790 207 217 76 97 95 0 2080 1964 1009 295 301 52 90 90 0 0.845 0.84 0.817 0.87 1.467 0.823 0.949 80 430 3293 3071 -0.243 1508 1785 1402 1669 0
Hs6-1-9-1 null 3650 18660 120 2861 4151 3584 208 217 76 100 98 0 3154 4458 3875 300 304 64 99 96 0 0.93 0.948 0.946 1.005 1.406 0.935 0.988 120 554 5507 8101 -0.105 2653 2854 3943 4158 0
Hs6-1-10-1 null 3820 18660 120 1092 1289 813 211 219 74 96 92 0 1116 1329 804 300 303 54 96 90 0 1.08 1.048 1.049 1.012 1.842 1.034 0.937 120 500 1697 2107 0.111 881 816 1078 1029 0
Hs6-1-11-1 null 3990 18660 120 1144 1611 1138 208 217 75 95 91 0 1757 2416 1788 290 295 49 96 96 0 0.638 0.66 0.661 0.642 1.495 0.645 0.962 120 553 2403 3529 -0.648 936 1467 1403 2126 0
Hs6-1-12-1 null 4170 18660 100 1331 1375 701 201 214 73 95 92 0 1907 1719 884 291 296 51 91 90 0 0.699 0.822 0.841 0.888 2.122 0.809 0.931 80 356 2746 2602 -0.516 1130 1616 1174 1428 0
Hs6-1-13-1 -0.122783 4350 18660 210 6921 6385 2077 204 214 74 100 99 0 6621 6012 1982 291 297 61 99 98 0 1.061 1.08 1.086 1.098 1.17 1.074 0.985 316 1764 13047 11902 0.086 6717 6330 6181 5721 0
Hs6-1-14-1 null 4510 18660 100 242 436 790 207 218 72 33 11 0 330 509 744 297 299 56 36 21 0 1.061 1.08 0.774 0.793 3.602 1.035 0.991 80 358 68 441 0.085 35 33 229 212 -50
Hs6-1-15-1 null 4700 18660 110 4817 4547 2276 206 218 73 98 96 0 4456 4198 2082 289 294 54 93 93 0 1.107 1.111 1.112 1.069 1.785 1.104 0.983 80 488 8778 8250 0.146 4611 4167 4341 3909 0
Hs6-1-16-1 null 4860 18660 100 961 938 438 212 220 74 88 87 0 1264 1246 593 288 293 52 91 90 0 0.767 0.758 0.775 0.785 1.472 0.747 0.874 80 438 1725 1684 -0.382 749 976 726 958 0
Hs6-1-17-1 0.201026 5040 18660 100 5594 5017 2936 216 219 69 98 97 0 4494 3933 2296 292 296 54 92 92 0 1.28 1.319 1.341 1.406 1.395 1.309 0.987 80 464 9580 8442 0.356 5378 4202 4801 3641 0
Hs6-1-18-1 null 5220 18660 100 1051 1041 455 209 213 64 95 92 0 1631 1433 675 291 294 54 88 88 0 0.628 0.729 0.74 0.793 2.386 0.705 0.908 80 415 2182 1974 -0.67 842 1340 832 1142 0
Hs6-1-19-1 null 5390 18660 120 2201 3568 2753 206 210 66 99 98 0 2084 3707 2955 290 291 51 97 97 0 1.112 0.984 1 1.043 1.247 0.957 0.988 120 532 3789 6779 0.153 1995 1794 3362 3417 0
Hs6-1-20-1 null 5570 18660 120 1315 1734 1237 207 214 69 98 96 0 1187 1692 1194 287 290 48 94 94 0 1.231 1.087 1.096 1.133 1.325 1.064 0.957 120 514 2008 2932 0.3 1108 900 1527 1405 0

Total number of rows: 20000

Table truncated, full table size 3699 Kbytes.




Supplementary data files not provided
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