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Sample GSM50307 Query DataSets for GSM50307
Status Public on Jan 02, 2006
Title WTA_LCM_NOR2
Sample type RNA
 
Channel 1
Source name LCM_NOR2, 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 2050 18410 80 494 488 164 230 238 82 82 73 0 614 542 191 89 91 20 100 100 0 0.503 0.57 0.557 0.545 1.705 0.623 0.558 52 340 789 711 -0.992 264 525 258 453 0
Hs6-1-2-1 null 2230 18400 90 586 590 214 236 245 85 90 76 0 549 530 187 95 96 23 100 98 0 0.771 0.814 0.822 0.743 1.871 0.92 0.688 52 400 804 789 -0.375 350 454 354 435 0
Hs6-1-3-1 null 2420 18410 90 255 263 75 251 257 85 19 1 0 229 210 87 93 95 19 82 75 0 0.029 0.103 0.533 0.599 5.061 3.41 0.018 52 398 140 129 -5.087 4 136 12 117 -50
Hs6-1-4-1 null 2580 18410 80 390 409 126 257 262 91 69 34 0 432 389 141 94 95 20 94 90 0 0.393 0.515 0.522 0.554 2.907 0.765 0.343 52 322 471 447 -1.346 133 338 152 295 0
Hs6-1-5-1 null 2760 18420 60 286 337 141 267 272 87 31 15 0 325 315 87 97 101 27 93 93 0 0.083 0.321 0.442 0.364 3.475 1.113 0.078 32 176 247 288 -3.585 19 228 70 218 0
Hs6-1-6-1 -0.430833 2940 18410 70 689 684 247 253 271 107 84 84 0 923 850 215 109 135 99 100 96 0 0.536 0.582 0.614 0.514 1.776 0.628 0.628 32 236 1250 1172 -0.901 436 814 431 741 0
Hs6-1-7-1 -0.119165 3110 18420 110 1573 1776 1039 263 274 95 97 95 0 2341 2306 1248 117 121 34 100 100 0 0.589 0.691 0.692 0.636 1.649 0.714 0.908 80 553 3534 3702 -0.764 1310 2224 1513 2189 0
Hs6-1-8-1 null 3280 18440 80 537 557 182 295 295 102 78 61 0 567 510 181 120 124 32 94 92 0 0.541 0.672 0.639 0.662 2.446 0.77 0.503 52 322 689 652 -0.885 242 447 262 390 0
Hs6-1-9-1 -0.963993 3460 18440 100 736 773 349 277 284 96 82 77 0 1381 1304 531 115 119 29 100 100 0 0.363 0.417 0.412 0.335 2.15 0.464 0.781 80 497 1725 1685 -1.464 459 1266 496 1189 0
Hs6-1-10-1 null 3640 18440 80 401 421 162 260 272 93 65 34 0 376 352 126 107 114 44 88 82 0 0.524 0.657 0.616 0.668 2.714 1.025 0.381 52 328 410 406 -0.932 141 269 161 245 0
Hs6-1-11-1 null 3820 18440 80 526 529 158 241 254 93 90 76 0 685 615 263 103 115 56 96 92 0 0.49 0.563 0.535 0.592 2.237 0.555 0.641 52 326 867 800 -1.03 285 582 288 512 0
Hs6-1-12-1 null 3990 18450 70 544 524 201 249 267 96 81 65 0 487 438 176 114 125 55 84 81 0 0.791 0.849 1.007 1.024 2.128 0.986 0.542 32 210 668 599 -0.338 295 373 275 324 0
Hs6-1-13-1 null 4160 18440 160 625 618 182 267 282 105 90 76 0 595 568 133 111 122 55 96 95 0 0.74 0.768 0.75 0.683 1.769 0.902 0.641 208 1026 842 808 -0.435 358 484 351 457 0
Hs6-1-14-1 -0.255393 4340 18440 110 761 794 366 260 276 100 88 77 0 844 829 303 101 113 57 98 98 0 0.674 0.734 0.694 0.626 2.122 0.831 0.775 80 506 1244 1262 -0.569 501 743 534 728 0
Hs6-1-15-1 -0.463198 4520 18440 70 620 639 217 270 291 112 93 75 0 686 658 156 107 126 73 100 100 0 0.604 0.67 0.62 0.632 1.605 0.816 0.515 32 236 929 920 -0.726 350 579 369 551 0
Hs6-1-16-1 null 4700 18450 70 370 368 102 265 274 98 50 21 0 380 369 98 106 114 48 93 93 0 0.383 0.392 0.396 0.402 3.552 0.849 0.161 32 236 379 366 -1.384 105 274 103 263 0
Hs6-1-17-1 -0.202506 4870 18440 90 767 730 285 261 268 95 84 76 0 784 714 282 100 102 24 96 96 0 0.74 0.764 0.726 0.654 1.721 0.848 0.77 52 404 1190 1083 -0.435 506 684 469 614 0
Hs6-1-18-1 null 5050 18450 90 349 350 117 261 272 103 38 15 0 313 274 113 98 107 56 80 67 0 0.409 0.506 0.653 0.639 4.817 1.03 0.178 52 327 303 265 -1.289 88 215 89 176 -50
Hs6-1-19-1 null 5220 18460 170 595 597 182 259 268 96 91 78 0 651 616 145 104 111 43 98 96 0 0.614 0.66 0.664 0.602 2.104 0.757 0.68 208 1079 883 850 -0.703 336 547 338 512 0
Hs6-1-20-1 0.205133 5400 18460 90 770 809 326 248 252 90 94 90 0 717 669 257 97 102 29 100 100 0 0.842 0.981 0.969 0.925 1.65 1.089 0.763 52 366 1142 1133 -0.248 522 620 561 572 0

Total number of rows: 20000

Table truncated, full table size 3429 Kbytes.




Supplementary data files not provided
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