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Sample GSM50339 Query DataSets for GSM50339
Status Public on Jan 02, 2006
Title WTA_LCM_STROMA2
Sample type RNA
 
Channel 1
Source name LCM_STROMA2, Benign stroma adjacent to cancerous epithelium isolated by LCM 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 1770 18930 100 1737 1716 596 265 283 109 100 100 0 1246 1203 397 146 148 28 100 100 0 1.338 1.373 1.362 1.353 1.24 1.4 0.949 80 496 2572 2508 0.42 1472 1100 1451 1057 0
Hs6-1-2-1 null 1940 18930 90 1327 1320 338 277 294 106 100 100 0 1316 1245 281 143 148 33 100 100 0 0.895 0.946 0.946 0.932 1.299 0.953 0.879 52 374 2223 2145 -0.16 1050 1173 1043 1102 0
Hs6-1-3-1 null 2130 18940 80 555 754 1262 282 300 123 80 55 0 414 468 509 139 142 29 94 94 0 0.993 1.435 1.095 0.961 2.133 2.534 0.887 52 314 548 801 -0.011 273 275 472 329 0
Hs6-1-4-1 null 2300 18930 110 1249 1204 411 277 291 110 97 91 0 1085 977 311 144 146 30 100 97 0 1.033 1.113 1.069 1.096 1.488 1.177 0.875 80 524 1913 1760 0.047 972 941 927 833 0
Hs6-1-5-1 null 2460 18940 90 742 746 166 276 293 103 98 92 0 698 678 180 144 147 31 98 98 0 0.841 0.88 0.856 0.871 1.444 0.939 0.706 52 353 1020 1004 -0.25 466 554 470 534 0
Hs6-1-6-1 null 2640 18930 100 1157 1110 381 284 319 271 90 80 0 1605 1440 512 149 154 40 100 100 0 0.6 0.64 0.601 0.599 1.664 0.644 0.853 80 445 2329 2117 -0.738 873 1456 826 1291 0
Hs6-1-7-1 -0.02585 2810 18930 110 5800 5598 1854 282 312 164 100 100 0 7758 6955 2539 157 176 144 100 100 0 0.726 0.782 0.788 0.805 1.256 0.759 0.962 80 510 13119 12114 -0.462 5518 7601 5316 6798 0
Hs6-1-8-1 null 2990 18930 110 1445 1455 375 287 317 148 100 98 0 1408 1320 331 159 180 144 100 100 0 0.927 1.006 1.005 1.001 1.376 1.023 0.867 80 497 2407 2329 -0.109 1158 1249 1168 1161 0
Hs6-1-9-1 0.058256 3160 18940 110 4299 3836 1549 292 301 111 100 100 0 4811 4257 1651 157 161 37 100 100 0 0.861 0.864 0.877 0.855 1.304 0.872 0.957 80 511 8661 7644 -0.216 4007 4654 3544 4100 0
Hs6-1-10-1 null 3340 18930 110 1066 1058 358 291 301 107 98 93 0 968 927 266 158 164 41 100 97 0 0.957 0.997 0.96 0.963 1.448 1.085 0.806 80 491 1585 1536 -0.064 775 810 767 769 0
Hs6-1-11-1 -0.536977 3510 18930 110 1583 1513 441 291 303 106 100 98 0 2147 1944 601 153 161 42 100 100 0 0.648 0.682 0.67 0.681 1.353 0.68 0.904 80 510 3286 3013 -0.626 1292 1994 1222 1791 0
Hs6-1-12-1 null 3690 18930 110 1108 1110 365 280 289 98 100 97 0 1107 1055 326 151 156 36 100 100 0 0.866 0.918 0.916 0.893 1.524 0.959 0.837 80 439 1784 1734 -0.207 828 956 830 904 0
Hs6-1-13-1 0.023044 3880 18940 200 2206 2128 538 287 295 97 99 99 0 2121 2042 479 154 160 40 100 100 0 0.976 0.975 0.972 0.959 1.261 0.996 0.944 316 1249 3886 3729 -0.036 1919 1967 1841 1888 0
Hs6-1-14-1 0.248229 4040 18940 90 3503 3237 868 284 307 99 100 100 0 3280 2962 835 155 162 44 100 100 0 1.03 1.052 1.058 1.06 1.201 1.03 0.941 52 275 6344 5760 0.043 3219 3125 2953 2807 0
Hs6-1-15-1 0.093127 4210 18940 100 1826 1811 683 284 296 97 100 100 0 1752 1631 662 158 165 41 100 100 0 0.967 1.037 1.042 1.069 1.357 1.038 0.929 80 447 3136 3000 -0.048 1542 1594 1527 1473 0
Hs6-1-16-1 null 4390 18940 100 774 764 200 278 283 93 98 91 0 766 748 210 154 159 40 100 100 0 0.81 0.818 0.848 0.804 1.45 0.874 0.769 80 464 1108 1080 -0.303 496 612 486 594 0
Hs6-1-17-1 0.070524 4560 18930 90 2443 2277 695 284 297 127 100 98 0 2281 2140 678 155 189 325 100 94 0 1.016 1.004 0.997 1.006 1.225 1.007 0.954 52 372 4285 3978 0.022 2159 2126 1993 1985 0
Hs6-1-18-1 null 4740 18940 100 899 893 271 283 298 123 93 88 0 786 734 233 155 185 314 81 51 0 0.976 1.054 1.035 1.002 1.605 1.11 0.82 80 398 1247 1189 -0.035 616 631 610 579 0
Hs6-1-19-1 -0.036973 4930 18940 200 2171 2137 547 282 295 102 100 99 0 2307 2183 519 160 168 109 100 100 0 0.88 0.917 0.93 0.902 1.27 0.927 0.942 316 1237 4036 3878 -0.185 1889 2147 1855 2023 0
Hs6-1-20-1 null 5090 18940 90 367 363 115 277 288 96 46 13 0 210 246 121 160 164 39 63 34 0 1.8 1 1.204 1.242 3.058 0.727 0.435 52 274 140 172 0.848 90 50 86 86 -50

Total number of rows: 20000

Table truncated, full table size 3612 Kbytes.




Supplementary data files not provided
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