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Sample GSM88428 Query DataSets for GSM88428
Status Public on Dec 21, 2005
Title ARD842, CAIS, F, GOF, 6 x 100nM DHT, 14d
Sample type RNA
 
Channel 1
Source name mixed reference (CRG + FR)
Organism Homo sapiens
Characteristics mixed reference (CRG + FR)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ARD842, G0, 6 x 100nM DHT, 14 days
Organism Homo sapiens
Characteristics ARD842, G0, 6 x 100nM DHT, 14 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15807.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 Dec 19, 2005
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 GPL3039
Series (2)
GSE3871 Effects of androgen treatment on genital fibroblasts
GSE4353 Genital fibroblasts of normal males and 46,XY females with androgen insensitivity syndrome

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
1 343 369 206 167 137 202 320 347 206 180 114 180 0 0 98 157 41 91 86 75 73 50 339 294 .678 1.474 1.579 1.347 1.344 2.643 52 368 3.225 .52 90 1760 9410 44 53 43 52 0 340 154 186 1.36 320 166 .735 1.457 .444 .543
2 450 639 219 167 231 472 450 558 215 175 231 391 0 0 185 326 45 89 78 87 65 84 703 622 .489 2.043 1.693 2.293 1.982 3.123 32 127 3.042 .63 60 1920 9440 49 55 61 67 0 589 154 435 1.885 515 361 .531 1.561 .914 .643
3 1577 1118 211 171 1366 947 1510 1139 214 179 1299 968 0 0 457 386 47 88 100 100 100 98 2313 2267 1.442 .693 .745 .662 .715 1.557 80 339 .826 .88 100 2040 9410 44 54 71 81 0 1031 158 874 .64 1051 893 1.564 .687 -.645 -.541
4 498 417 216 176 282 241 506 407 215 179 290 231 0 0 97 216 41 96 100 66 100 50 523 521 1.17 .855 .797 .735 1.089 2.768 12 79 2.724 .48 50 2180 9440 49 54 87 92 0 385 162 222 .788 375 213 1.268 .735 -.343 -.445
5 1256 3938 214 180 1042 3758 1223 3799 215 192 1009 3619 0 0 268 1395 47 96 100 100 100 100 4800 4628 .277 3.607 3.587 3.452 3.413 1.468 80 452 4.115 .91 110 2300 9410 43 54 96 107 0 3633 166 3467 3.327 3504 3338 .301 3.309 1.734 1.726
6 359 375 205 159 154 216 343 380 212 179 138 221 0 0 54 124 43 92 100 83 83 58 370 359 .713 1.403 1.601 1.252 1.47 2.511 12 84 3.972 .45 50 2450 9440 49 54 114 119 0 346 147 199 1.294 351 204 .773 1.477 .372 .563
7 1070 722 213 173 857 549 988 645 216 184 775 472 0 0 336 368 49 87 100 95 100 92 1406 1247 1.561 .641 .609 .558 .596 1.713 80 360 .876 .85 110 2570 9420 44 55 123 134 0 666 160 506 .591 595 435 1.692 .562 -.759 -.832
8 1307 2244 220 177 1087 2067 1287 1966 222 188 1067 1789 0 0 351 938 47 94 100 100 100 100 3154 2856 .526 1.902 1.677 1.817 1.877 1.399 80 309 2.187 .91 100 2700 9420 45 55 137 147 0 2070 163 1907 1.754 1814 1650 .57 1.547 .811 .629
9 851 560 223 200 628 360 824 521 232 204 601 321 0 0 231 200 52 93 100 90 100 81 988 922 1.744 .573 .534 .495 .497 1.934 32 136 1.097 .65 70 2860 9420 46 53 154 161 0 517 184 332 .529 481 296 1.891 .493 -.919 -1.021
10 284 270 229 196 55 74 285 250 234 208 56 54 0 0 65 113 49 98 53 36 26 15 129 110 .743 1.345 .964 1.38 1.549 3.711 120 367 8.774 .2 120 2970 9420 44 56 163 175 0 249 181 68 1.241 231 50 .806 .89 .312 -.169
11 1159 328 232 188 927 140 1177 314 234 205 945 126 0 0 236 192 47 101 100 53 100 25 1067 1071 6.621 .151 .133 .138 .18 2.807 80 244 .811 .43 100 3110 9420 45 55 178 188 0 303 173 129 .139 290 116 7.178 .123 -2.844 -3.023
12 557 782 228 196 329 586 549 642 231 217 321 446 0 0 153 420 47 93 98 100 96 86 915 767 .561 1.781 1.389 1.61 1.61 1.829 52 253 2.69 .76 90 3240 9410 44 53 191 200 0 721 181 541 1.643 592 411 .609 1.282 .716 .358
13 558 486 237 201 321 285 551 458 244 224 314 257 0 0 129 214 69 105 97 83 95 60 606 571 1.126 .888 .818 .846 .866 1.995 80 292 1.854 .62 100 3390 9420 45 55 206 216 0 448 185 263 .819 422 237 1.221 .755 -.288 -.405
14 548 462 238 199 310 263 542 461 247 220 304 262 0 0 121 174 73 110 97 75 91 58 573 566 1.179 .848 .862 .76 .832 2.419 80 237 1.944 .55 100 3520 9420 45 55 219 229 0 426 184 243 .783 425 242 1.278 .795 -.354 -.331
15 458 444 238 205 220 239 421 382 240 223 183 177 0 0 200 260 52 108 77 64 66 40 459 360 .921 1.086 .967 1.159 1.193 3.425 120 323 1.738 .73 120 3650 9420 44 56 231 243 0 410 189 220 1.002 352 163 .998 .892 .003 -.165
16 1191 757 249 202 942 555 1179 690 251 223 930 488 0 0 291 339 52 108 100 93 100 88 1497 1418 1.697 .589 .525 .506 .573 2.085 80 233 .914 .77 100 3790 9410 44 54 246 256 0 698 186 512 .543 637 450 1.84 .484 -.88 -1.047
17 745 802 238 191 507 611 722 794 242 211 484 603 0 0 187 376 49 98 100 92 97 87 1118 1087 .83 1.205 1.246 1.066 1.274 2.042 80 241 1.71 .81 100 3920 9410 44 54 259 269 0 740 176 564 1.112 732 556 .9 1.149 .153 .201
18 431 306 234 203 197 103 428 290 240 212 194 87 0 0 152 148 48 90 78 49 69 27 300 281 1.913 .523 .448 .752 .711 2.658 120 350 1.914 .48 120 4050 9420 44 56 271 283 0 282 187 95 .482 268 80 2.073 .414 -1.052 -1.273
19 559 692 246 220 313 472 530 634 246 226 284 414 0 0 161 318 50 106 97 92 93 78 785 698 .663 1.508 1.458 1.396 1.633 2.211 80 312 2.298 .74 110 4200 9410 43 54 286 297 0 638 203 435 1.391 585 382 .719 1.345 .476 .427
20 1535 1424 232 202 1303 1222 1495 1407 234 220 1263 1205 0 0 266 415 52 110 100 100 100 100 2525 2468 1.066 .938 .954 .9 .943 1.331 52 200 1.07 .89 90 4330 9400 43 52 300 309 0 1314 186 1127 .865 1298 1112 1.156 .88 -.209 -.184

Total number of rows: 44544

Table truncated, full table size 9600 Kbytes.




Supplementary data files not provided

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