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Sample GSM50338 Query DataSets for GSM50338
Status Public on Jan 02, 2006
Title WTA_LCM_STROMA1
Sample type RNA
 
Channel 1
Source name LCM_STROMA1, 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 1810 18630 100 846 880 335 231 239 91 97 95 0 970 941 394 155 162 60 98 95 0 0.755 0.826 0.84 0.865 1.552 0.825 0.82 80 471 1430 1435 -0.406 615 815 649 786 0
Hs6-1-2-1 null 1970 18640 100 1108 992 436 233 238 85 92 88 0 868 934 523 156 164 50 91 85 0 1.229 0.976 0.963 1.072 2.112 0.929 0.863 80 436 1587 1537 0.297 875 712 759 778 0
Hs6-1-3-1 null 2160 18640 60 350 353 109 238 247 93 59 28 0 533 456 155 150 166 60 87 87 0 0.292 0.376 0.365 0.413 2.493 0.433 0.054 32 171 495 421 -1.774 112 383 115 306 0
Hs6-1-4-1 null 2320 18630 120 854 957 464 239 253 89 94 88 0 699 737 437 164 176 66 85 81 0 1.15 1.253 1.22 1.359 2.294 1.197 0.823 120 641 1150 1291 0.201 615 535 718 573 0
Hs6-1-5-1 null 2490 18640 80 497 514 141 236 244 80 92 80 0 614 559 238 160 162 39 90 82 0 0.575 0.697 0.615 0.665 2.586 0.655 0.513 52 286 715 677 -0.799 261 454 278 399 0
Hs6-1-6-1 null 2670 18640 110 1137 1149 531 231 236 82 97 90 0 1602 1432 747 164 170 50 96 93 0 0.63 0.724 0.729 0.745 1.896 0.701 0.872 80 468 2344 2186 -0.666 906 1438 918 1268 0
Hs6-1-7-1 -0.034419 2840 18630 120 4452 5072 3270 252 269 286 96 91 0 4691 5120 3314 172 182 59 100 99 0 0.929 0.974 0.986 0.981 1.786 0.983 0.935 120 572 8719 9768 -0.106 4200 4519 4820 4948 0
Hs6-1-8-1 null 3020 18630 110 1157 1166 688 268 292 313 82 68 0 1231 1079 555 175 193 69 91 90 0 0.842 0.993 0.967 0.989 1.8 1.102 0.804 80 470 1945 1802 -0.248 889 1056 898 904 0
Hs6-1-9-1 null 3190 18640 120 1623 2024 1434 271 285 108 96 91 0 1964 2355 1783 169 193 81 94 92 0 0.753 0.802 0.818 0.856 2.46 0.803 0.949 120 560 3147 3939 -0.409 1352 1795 1753 2186 0
Hs6-1-10-1 null 3360 18630 110 1168 1097 450 266 282 115 91 87 0 1056 922 444 165 181 70 86 85 0 1.012 1.098 1.062 1.058 2.427 1.119 0.822 80 472 1793 1588 0.018 902 891 831 757 0
Hs6-1-11-1 null 3540 18630 110 1599 1386 715 258 271 103 91 82 0 1749 1516 878 168 179 65 88 85 0 0.848 0.837 0.838 0.823 1.929 0.831 0.892 80 506 2922 2476 -0.238 1341 1581 1128 1348 0
Hs6-1-12-1 null 3720 18640 100 1127 1118 443 255 265 89 97 95 0 1088 994 518 165 176 61 85 83 0 0.945 1.041 1.009 1.125 2.014 0.984 0.869 80 362 1795 1692 -0.082 872 923 863 829 0
Hs6-1-13-1 -0.30569 3910 18630 210 2705 2670 789 281 293 105 99 98 0 3067 2928 814 215 227 86 99 97 0 0.85 0.881 0.878 0.897 1.334 0.889 0.945 316 1790 5276 5102 -0.235 2424 2852 2389 2713 0
Hs6-1-14-1 null 4080 18630 90 248 266 102 270 280 99 15 5 0 179 173 57 198 205 59 3 0 0 1.158 0.16 1.974 1.483 5.382 5.778 0.022 52 285 -41 -29 0.212 -22 -19 -4 -25 -50
Hs6-1-15-1 null 4250 18640 110 1112 1084 433 262 273 102 96 96 0 1236 1226 638 187 197 69 95 92 0 0.81 0.791 0.771 0.87 1.61 0.765 0.835 80 484 1899 1861 -0.303 850 1049 822 1039 0
Hs6-1-16-1 null 4420 18630 100 768 756 251 253 260 91 90 88 0 850 791 331 172 178 55 88 87 0 0.76 0.813 0.782 0.831 1.618 0.805 0.777 80 440 1193 1122 -0.397 515 678 503 619 0
Hs6-1-17-1 -0.202465 4590 18630 100 1988 1867 800 254 265 92 97 95 0 2149 1844 850 167 176 51 96 93 0 0.875 0.962 1 1.028 1.727 0.958 0.909 80 452 3716 3290 -0.193 1734 1982 1613 1677 0
Hs6-1-18-1 null 4770 18630 100 1100 1052 353 265 273 95 100 92 0 908 818 359 169 182 55 90 83 0 1.13 1.213 1.269 1.437 2.308 1.176 0.83 80 390 1574 1436 0.176 835 739 787 649 0
Hs6-1-19-1 -0.418654 4950 18630 190 2671 2661 620 275 285 99 100 100 0 3313 3169 754 199 207 68 100 100 0 0.769 0.803 0.805 0.815 1.252 0.799 0.954 256 1419 5510 5356 -0.378 2396 3114 2386 2970 0
Hs6-1-20-1 null 5130 18630 90 392 403 128 270 279 99 53 28 0 222 272 143 171 188 65 44 28 0 2.392 1.317 0.978 1.034 4.244 2.225 0.129 52 314 173 234 1.258 122 51 133 101 -50

Total number of rows: 20000

Table truncated, full table size 3609 Kbytes.




Supplementary data files not provided
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