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Sample GSM91645 Query DataSets for GSM91645
Status Public on Jan 11, 2006
Title GVNBPHF11_T24_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_T24_T total RNA
Organism Homo sapiens
Characteristics GVNBPHF11_T24_T total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35626.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
1 357 338 111 171 246 167 350 351 118 176 239 180 0 0 88 124 32 68 100 75 93 65 413 419 1.473 .679 .753 .682 .807 2.433 32 166 .894 .54 60 1810 9230 32 38 22 28 0 402 204 199 .808 418 214 1.237 .897 -.307 -.157
2 3435 607 116 180 3319 427 3489 635 125 191 3373 455 0 0 805 171 67 84 100 93 100 90 3746 3828 7.773 .129 .135 .119 .136 1.805 32 220 .121 .84 70 1960 9230 31 38 36 43 0 723 214 508 .153 756 542 6.529 .161 -2.707 -2.639
3 2656 1084 113 182 2543 902 2881 1103 120 184 2768 921 0 0 715 334 35 71 100 100 100 100 3445 3689 2.819 .355 .333 .346 .354 1.274 12 104 .383 .88 50 2090 9220 31 36 50 55 0 1290 217 1074 .422 1313 1096 2.368 .396 -1.244 -1.336
4 847 371 115 177 732 194 884 378 118 181 769 201 0 0 309 125 28 69 96 78 96 65 926 970 3.773 .265 .261 .257 .272 1.924 32 165 .222 .66 60 2240 9230 32 38 65 71 0 442 211 231 .316 450 239 3.169 .311 -1.664 -1.684
5 1012 2603 111 191 901 2412 1059 2814 113 200 948 2623 0 0 481 1067 25 76 94 100 92 100 3313 3571 .374 2.677 2.767 2.929 2.664 2.031 52 278 2.692 .93 80 2390 9230 31 39 79 87 0 3099 227 2871 3.187 3350 3123 .314 3.294 1.672 1.72
6 574 396 111 192 463 204 588 374 114 202 477 182 0 0 161 133 26 80 100 81 100 62 667 659 2.27 .441 .382 .372 .44 2.348 32 221 .523 .67 70 2530 9220 30 37 93 100 0 471 229 243 .525 445 217 1.906 .454 -.931 -1.139
7 1974 1538 118 174 1856 1364 2046 1428 118 188 1928 1254 0 0 687 527 27 73 100 100 100 100 3220 3182 1.361 .735 .65 .746 .702 1.628 32 212 .683 .9 70 2690 9230 31 38 109 116 0 1831 207 1624 .875 1700 1493 1.143 .774 -.193 -.369
8 588 710 116 194 472 516 624 700 118 200 508 506 0 0 245 287 29 77 94 94 92 88 988 1014 .915 1.093 .996 1.173 1.042 2.522 52 280 1.17 .84 80 2830 9230 31 39 123 131 0 845 231 614 1.301 833 602 .768 1.186 .38 .246
9 548 449 114 197 434 252 557 462 137 209 443 265 0 0 134 145 265 86 86 90 25 65 686 708 1.722 .581 .598 .533 .587 1.922 52 278 .655 .72 80 2980 9220 30 38 138 146 0 535 235 300 .691 550 315 1.447 .712 -.533 -.49
10 353 328 116 185 237 143 361 332 129 191 245 147 0 0 104 105 74 74 93 71 75 50 380 392 1.657 .603 .6 .541 .64 2.852 32 158 .826 .6 60 3130 9230 32 38 154 160 0 390 220 170 .718 395 175 1.392 .714 -.477 -.485
11 1615 2603 115 191 1500 2412 1642 2650 117 198 1527 2459 0 0 535 727 27 81 100 100 100 100 3912 3986 .622 1.608 1.61 1.723 1.57 1.645 52 282 1.581 .94 80 3270 9230 31 39 167 175 0 3099 227 2871 1.914 3155 2927 .522 1.917 .937 .939
12 5705 5212 119 190 5586 5022 5919 5402 126 206 5800 5212 0 0 2632 1942 52 80 100 100 100 100 10608 11012 1.112 .899 .899 .927 .875 1.498 32 214 .855 .92 70 3410 9220 30 37 181 188 0 6205 226 5979 1.07 6431 6205 .934 1.07 .098 .097
13 1156 4039 117 194 1039 3845 1163 4079 123 202 1046 3885 0 0 241 914 44 79 100 100 100 100 4884 4931 .27 3.701 3.714 3.679 3.873 1.31 52 337 3.841 .85 90 3560 9220 29 38 195 204 0 4808 231 4577 4.406 4856 4625 .227 4.422 2.139 2.145
14 378 370 117 197 261 173 375 370 121 201 258 173 0 0 87 131 28 79 98 76 98 51 434 431 1.509 .663 .671 .623 .772 2.491 52 313 .987 .54 90 3710 9230 30 39 210 219 0 440 235 206 .789 440 206 1.267 .798 -.342 -.325
15 537 497 120 207 417 290 558 478 123 214 438 271 0 0 120 137 30 87 98 92 98 82 707 709 1.438 .695 .619 .618 .685 1.838 52 254 .76 .75 80 3860 9230 31 39 226 234 0 592 246 345 .828 569 323 1.208 .737 -.272 -.441
16 7159 9423 124 209 7035 9214 7319 9997 127 217 7195 9788 0 0 2025 2642 31 82 100 100 100 100 16249 16983 .764 1.31 1.36 1.316 1.297 1.274 52 335 1.308 .96 90 4000 9220 29 38 239 248 0 11218 249 10969 1.559 11901 11652 .641 1.62 .641 .696
17 1750 6758 120 196 1630 6562 1839 7511 123 208 1719 7315 0 0 783 2854 26 80 100 100 100 100 8192 9034 .248 4.026 4.255 4.265 4.031 1.939 52 264 4.082 .95 80 4150 9230 31 39 255 263 0 8045 233 7812 4.793 8942 8708 .209 5.066 2.261 2.341
18 173 247 118 197 55 50 127 215 121 206 9 18 0 0 147 142 25 79 32 28 21 9 105 27 1.1 .909 2 2.077 1.754 3.743 52 256 1.708 .5 80 4300 9220 30 38 270 278 -50 294 235 60 1.082 256 21 .924 2.381 .114 1.252
19 4184 3125 115 202 4069 2923 4452 3223 119 204 4337 3021 0 0 1105 774 28 73 100 100 98 100 6992 7358 1.392 .718 .697 .778 .7 1.906 52 254 .697 .94 80 4440 9230 31 39 284 292 0 3720 240 3480 .855 3837 3596 1.169 .829 -.226 -.27
20 1866 1163 116 194 1750 969 1969 1180 118 200 1853 986 0 0 585 283 28 83 100 100 98 100 2719 2839 1.806 .554 .532 .599 .523 1.902 52 316 .501 .91 90 4590 9230 30 39 298 307 0 1385 231 1154 .659 1405 1174 1.517 .633 -.601 -.659

Total number of rows: 43104

Table truncated, full table size 9473 Kbytes.




Supplementary data files not provided
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