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Sample GSM50341 Query DataSets for GSM50341
Status Public on Jan 02, 2006
Title Tissue_Unamp2
Sample type RNA
 
Channel 1
Source name PCA1, localized prostate adenocarcinoma tissue sample, 30 ug total RNA, Cy5
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name CPP, Commercially available pool of benign prostate tissue total RNA, 30 ug total RNA, Cy3
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description See 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 GPL2012
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
Hs3-1-1-1 -0.091305 2120 18040 80 7352 7214 3299 1334 1159 648 96 88 0 10601 10573 4868 2007 1826 854 92 92 0 0.7 0.686 0.566 0.532 2.488 0.615 0.413 52 318 14612 14446 -0.514 6018 8594 5880 8566 0
Hs3-1-2-1 -1.572159 2300 18040 90 6539 7525 4671 1116 945 558 96 90 0 21727 24458 14570 1844 1642 725 98 96 0 0.273 0.283 0.209 0.283 4.03 0.25 0.47 52 324 25306 29023 -1.874 5423 19883 6409 22614 0
Hs3-1-3-1 null 2480 18020 100 1125 1311 620 1297 1325 272 35 21 0 2826 2895 1397 2033 2066 378 57 50 0 -0.217 0.016 0.468 0.454 3.369 0.153 0.078 80 440 621 876 Error -172 793 14 862 -50
Hs3-1-4-1 -1.011002 2630 18040 90 4822 4846 1893 1249 1283 384 98 88 0 12549 13042 6137 1987 2007 414 96 96 0 0.338 0.325 0.298 0.314 2.762 0.262 0.488 52 374 14135 14652 -1.564 3573 10562 3597 11055 0
Hs3-1-5-1 -1.093991 2810 18040 60 2919 3079 580 1146 1068 517 100 96 0 8921 9173 3339 1651 1688 1038 96 96 0 0.244 0.257 0.261 0.28 1.699 0.166 0.376 32 164 9043 9455 -2.036 1773 7270 1933 7522 0
Hs3-1-6-1 -0.023089 3000 18030 110 11431 10895 5040 1205 1280 1082 95 92 0 17777 16758 8666 1688 1777 691 96 95 0 0.636 0.643 0.613 0.651 3.083 0.558 0.605 80 499 26315 24760 -0.654 10226 16089 9690 15070 0
Hs3-1-7-1 -0.719718 3170 18030 130 11497 14876 11844 1141 1168 307 99 96 0 28863 31661 21785 1720 1740 232 99 98 16 0.382 0.459 0.387 0.412 3.632 0.411 0.572 120 602 37499 43676 -1.39 10356 27143 13735 29941 0
Hs3-1-8-1 -0.703718 3350 18020 130 4081 5231 3256 1084 1092 229 98 97 0 8079 12293 10460 1685 1721 318 87 85 0 0.469 0.391 0.344 0.389 3.435 0.258 0.495 120 640 9391 14755 -1.093 2997 6394 4147 10608 0
Hs3-1-9-1 0.712253 3520 18020 120 4542 6195 4300 1024 1057 271 100 98 0 5498 6359 4635 1589 1605 228 86 84 0 0.9 1.084 0.893 1.178 3.631 0.981 0.575 120 560 7427 9941 -0.152 3518 3909 5171 4770 0
Hs3-1-10-1 null 3690 18030 120 2122 2473 1377 992 1017 216 82 66 0 4773 5474 3949 1543 1549 201 84 81 0 0.35 0.377 0.371 0.402 4.078 0.262 0.47 120 538 4360 5412 -1.515 1130 3230 1481 3931 0
Hs3-1-11-1 -0.667143 3880 18020 130 3021 4042 3062 908 922 188 90 82 0 5863 9458 8561 1486 1505 302 90 88 0 0.483 0.393 0.339 0.337 3.702 0.295 0.568 120 621 6490 11106 -1.051 2113 4377 3134 7972 0
Hs3-1-12-1 -1.092617 4050 18030 130 3433 4222 3294 886 925 247 85 75 0 7065 10840 9353 1476 1599 649 89 86 0 0.456 0.356 0.258 0.238 3.691 0.266 0.504 120 534 8136 12700 -1.134 2547 5589 3336 9364 0
Hs3-1-13-1 -0.479926 4230 18030 160 17577 14946 5518 865 931 306 100 100 0 37870 32795 9967 1459 1663 847 98 98 0 0.459 0.449 0.472 0.426 2.461 0.407 0.659 208 795 53123 45417 -1.123 16712 36411 14081 31336 0
Hs3-1-14-1 0.192815 4390 18020 140 3884 7147 7081 838 875 309 87 82 0 5662 9891 10016 1403 1534 762 75 66 0 0.715 0.743 0.622 0.868 4.988 0.595 0.586 156 691 7305 14797 -0.484 3046 4259 6309 8488 0
Hs3-1-15-1 -0.335988 4590 18030 90 3093 3159 1233 837 822 228 100 98 0 5640 5630 3037 1314 1322 290 88 88 0 0.521 0.538 0.427 0.476 2.337 0.403 0.493 52 336 6582 6638 -0.939 2256 4326 2322 4316 0
Hs3-1-16-1 0.118206 4750 18020 130 5465 7518 5807 788 788 161 100 98 0 6443 10305 8641 1268 1279 180 91 91 0 0.904 0.745 0.613 0.701 4.156 0.627 0.56 120 610 9852 15767 -0.146 4677 5175 6730 9037 0
Hs3-1-17-1 0.86029 4930 18020 120 8065 13519 13286 774 777 156 96 96 0 6234 12416 13084 1224 1244 192 87 85 0 1.455 1.139 1.068 1.176 4.052 1.075 0.573 120 549 12301 23937 0.541 7291 5010 12745 11192 0
Hs3-1-18-1 -0.423459 5110 18020 100 4463 4768 2198 763 774 162 100 100 0 8610 8871 5552 1189 1218 220 95 93 0 0.499 0.521 0.431 0.56 2.777 0.378 0.547 80 382 11121 11687 -1.004 3700 7421 4005 7682 0
Hs3-1-19-1 -0.697901 5270 18020 140 6013 9050 7613 680 688 156 99 98 0 14269 19864 17378 1147 1153 162 93 92 0 0.406 0.447 0.376 0.498 5.298 0.351 0.54 156 640 18455 27087 -1.299 5333 13122 8370 18717 0
Hs3-1-20-1 null 5450 18020 120 1855 2898 2417 674 677 155 89 78 0 4194 6154 5235 1097 1103 149 88 85 0 0.381 0.44 0.345 0.412 4.019 0.35 0.497 120 510 4278 7281 -1.391 1181 3097 2224 5057 0

Total number of rows: 20000

Table truncated, full table size 3793 Kbytes.




Supplementary data files not provided
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