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Sample GSM91635 Query DataSets for GSM91635
Status Public on Jan 11, 2006
Title GVNBPHF11_T2_T
Sample type RNA
 
Channel 1
Source name Stratagene universal RNA
Organism Homo sapiens
Characteristics Stratagene universal RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name GVNBPHF11_T2_T total RNA
Organism Homo sapiens
Characteristics GVNBPHF11_T2_T total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35622.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3341
Series (1)
GSE4010 Molecular targets of doxazosin in human prostatic stromal cells

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 655 436 177 183 478 253 645 441 178 197 468 258 0 0 285 192 43 86 90 75 87 62 731 726 1.889 .529 .551 .592 .606 1.942 32 164 .526 .8 60 1820 9140 19 25 23 29 0 566 238 329 .687 573 335 1.455 .716 -.541 -.482
2 3609 651 198 185 3411 466 3725 522 262 193 3527 337 0 0 2366 326 140 78 96 93 90 84 3877 3864 7.32 .137 .096 .149 .148 2.304 32 218 .125 .86 70 1970 9140 18 25 37 44 0 845 240 605 .177 678 438 5.636 .124 -2.495 -3.011
3 1485 1124 381 202 1104 922 517 281 369 210 136 79 0 0 2319 1808 99 76 59 50 36 40 2026 215 1.197 .835 .581 .759 .897 3.049 52 310 .783 .96 80 2110 9150 19 27 51 59 -50 1460 262 1197 1.085 365 103 .922 .754 .117 -.407
4 1514 482 390 227 1124 255 1441 434 404 228 1051 207 0 0 376 232 90 81 100 83 100 58 1379 1258 4.408 .227 .197 .163 .187 2.1 12 54 .265 .74 40 2270 9130 19 23 69 73 0 626 295 331 .295 564 269 3.394 .256 -1.763 -1.967
5 1807 4892 392 220 1415 4672 2119 5461 396 230 1727 5241 0 0 713 2245 64 103 100 100 96 100 6087 6968 .303 3.302 3.035 3.46 3.487 1.647 32 170 3.462 .94 60 2410 9150 20 26 82 88 0 6353 286 6068 4.288 7092 6806 .233 3.941 2.1 1.979
6 751 412 361 204 390 208 698 352 332 214 337 148 0 0 290 232 143 89 73 61 53 42 598 485 1.875 .533 .439 .531 .556 2.895 52 297 .566 .67 80 2550 9150 19 27 95 103 -50 535 265 270 .693 457 192 1.444 .57 -.53 -.81
7 2800 1819 60 153 2740 1666 3109 1858 85 166 3049 1705 0 0 1160 607 59 86 100 100 100 100 4406 4754 1.645 .608 .559 .632 .571 1.499 12 104 .554 .93 50 2700 9150 20 25 111 116 0 2362 199 2164 .79 2413 2214 1.266 .726 -.341 -.461
8 1263 1112 162 192 1101 920 1299 1247 179 207 1137 1055 0 0 294 403 176 117 100 100 100 91 2021 2192 1.197 .836 .928 .768 .984 1.674 12 98 .858 .89 50 2850 9140 19 24 126 131 0 1444 249 1195 1.085 1619 1370 .921 1.205 .118 .269
9 1008 558 211 215 797 343 981 520 221 219 770 305 0 0 239 252 100 84 100 93 100 75 1140 1075 2.324 .43 .396 .378 .381 1.925 32 226 .459 .76 70 2990 9150 19 26 139 146 0 725 279 445 .559 675 396 1.789 .514 -.839 -.959
10 798 382 348 231 450 151 800 368 346 241 452 137 0 0 178 129 87 88 100 71 96 37 601 589 2.98 .336 .303 .311 .287 2.215 32 170 .358 .55 60 3130 9150 20 26 154 160 0 496 300 196 .436 478 178 2.295 .394 -1.198 -1.345
11 1942 3803 303 210 1639 3593 1903 4017 283 214 1600 3807 0 0 584 1291 103 86 98 100 98 100 5232 5407 .456 2.192 2.379 2.129 2.293 1.481 52 288 2.278 .95 80 3270 9150 19 27 167 175 0 4939 273 4666 2.847 5217 4944 .351 3.09 1.509 1.628
12 6657 6449 151 188 6506 6261 5642 6393 158 195 5491 6205 0 0 4324 4111 52 76 100 100 100 100 12767 11696 1.039 .962 1.13 1.016 1.027 1.466 32 213 .949 .96 70 3420 9150 19 26 182 189 0 8375 244 8131 1.25 8303 8058 .8 1.468 .322 .553
13 1196 4851 107 165 1089 4686 1214 4871 105 170 1107 4706 0 0 271 996 57 71 100 100 100 100 5775 5813 .232 4.303 4.251 4.363 4.381 1.284 52 278 4.336 .95 80 3560 9150 19 27 196 204 0 6300 214 6086 5.588 6326 6112 .179 5.521 2.482 2.465
14 583 455 51 149 532 306 589 441 71 155 538 292 0 0 133 148 46 71 100 94 98 88 838 830 1.739 .575 .543 .501 .537 2.225 52 266 .627 .81 80 3710 9150 19 27 211 219 0 591 194 397 .747 573 379 1.339 .705 -.421 -.505
15 664 509 137 177 527 332 707 495 135 187 570 318 0 0 167 169 39 78 98 94 98 84 859 888 1.587 .63 .558 .563 .611 1.826 52 264 .68 .81 80 3850 9150 19 27 225 233 0 661 230 431 .818 643 413 1.222 .725 -.29 -.465
16 10517 14623 134 185 10383 14438 10833 15501 138 200 10699 15316 0 0 4184 5192 31 87 100 100 100 100 24821 26015 .719 1.391 1.432 1.477 1.393 1.607 52 289 1.359 .98 80 4000 9150 19 27 240 248 0 18991 240 18751 1.806 20131 19891 .554 1.859 .853 .895
17 3073 4210 133 183 2940 4027 3146 4135 139 197 3013 3952 0 0 612 825 38 78 100 100 100 100 6967 6965 .73 1.37 1.312 1.374 1.41 1.196 32 212 1.352 .97 70 4140 9140 18 25 254 261 0 5468 238 5230 1.779 5370 5132 .562 1.703 .831 .768
18 330 393 131 177 199 216 165 227 137 180 34 50 0 0 802 494 38 74 48 42 30 25 415 84 .921 1.085 1.471 1.719 1.769 2.81 52 256 .245 .22 80 4290 9140 18 26 269 277 -50 510 230 281 1.41 295 65 .709 1.91 .495 .933
19 5503 4190 137 171 5366 4019 5929 4478 140 179 5792 4307 0 0 1666 1318 32 73 100 100 100 100 9385 10099 1.335 .749 .744 .748 .739 1.178 52 254 .747 .98 80 4430 9150 19 27 283 291 0 5442 222 5219 .973 5816 5594 1.028 .966 -.04 -.05
20 2395 1746 135 182 2260 1564 2492 1676 140 190 2357 1494 0 0 920 735 32 77 100 100 100 98 3824 3851 1.445 .692 .634 .691 .658 1.494 52 266 .703 .95 80 4580 9150 19 27 298 306 0 2268 236 2031 .899 2177 1940 1.113 .823 -.154 -.281

Total number of rows: 43104

Table truncated, full table size 9501 Kbytes.




Supplementary data files not provided
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