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Sample GSM88430 Query DataSets for GSM88430
Status Public on Dec 21, 2005
Title ARD842, CAIS, F, GOF, 6 x ETOH, 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 ETOH, 14 days
Organism Homo sapiens
Characteristics ARD842, G0, 6 x ETOH, 14 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15743.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
1 411 362 242 193 169 169 404 341 250 254 162 148 0 0 83 156 72 452 88 5 55 0 338 310 1 1 .914 .886 1.092 3.473 52 341 3.863 .37 90 1950 9240 51 60 46 55 0 314 167 147 .867 296 128 1.153 .792 -.205 -.336
2 674 1299 253 257 421 1042 642 1253 292 362 389 996 0 0 160 283 163 807 91 91 91 8 1463 1385 .404 2.475 2.56 2.566 2.482 1.394 12 83 6.06 .38 50 2100 9260 55 60 63 68 0 1127 223 904 2.147 1087 864 .466 2.221 1.102 1.151
3 2983 2198 264 195 2719 2003 2953 1992 275 207 2689 1797 0 0 931 1088 86 90 100 97 100 96 4722 4486 1.357 .737 .668 .644 .726 1.794 80 368 .879 .93 100 2220 9220 49 59 73 83 0 1906 169 1737 .639 1728 1559 1.565 .58 -.646 -.787
4 925 932 278 193 647 739 1027 961 277 206 749 768 0 0 394 538 56 100 91 83 83 83 1386 1517 .876 1.142 1.025 1.051 1.104 1.926 12 83 1.346 .85 50 2350 9240 53 58 88 93 0 808 167 641 .991 834 666 1.009 .889 -.014 -.169
5 1800 6721 270 210 1530 6511 1751 6343 277 218 1481 6133 0 0 490 2250 64 99 100 100 100 100 8041 7614 .235 4.256 4.141 4.236 4.186 1.281 80 413 4.489 .91 110 2480 9230 49 60 98 109 0 5829 182 5647 3.691 5502 5319 .271 3.592 1.884 1.845
6 730 784 287 202 443 582 790 809 288 211 503 607 0 0 206 261 66 88 91 100 91 100 1025 1110 .761 1.314 1.207 1.417 1.307 1.665 12 89 1.534 .81 50 2610 9240 53 58 114 119 0 680 175 505 1.139 702 526 .878 1.047 .188 .066
7 1658 1018 281 185 1377 833 1695 1044 267 199 1414 859 0 0 462 362 101 98 100 100 100 96 2210 2273 1.653 .605 .607 .577 .591 1.423 80 306 .707 .9 100 2740 9230 50 60 125 135 0 883 160 723 .525 906 745 1.906 .527 -.93 -.924
8 2009 3505 74 159 1935 3346 1949 3370 152 172 1875 3211 0 0 561 1213 134 91 100 100 100 100 5281 5086 .578 1.729 1.713 1.695 1.659 1.263 80 280 1.965 .93 100 2870 9230 50 60 138 148 0 3040 138 2902 1.5 2923 2785 .667 1.485 .585 .571
9 835 624 56 141 779 483 783 535 99 158 727 394 0 0 551 342 106 93 86 88 80 80 1262 1121 1.613 .62 .542 .747 .637 3.271 52 196 .811 .78 80 3020 9230 51 59 154 162 0 541 122 419 .538 464 342 1.86 .47 -.895 -1.089
10 406 277 51 143 355 134 391 267 89 151 340 124 0 0 105 103 98 80 100 72 97 33 489 464 2.649 .377 .365 .323 .36 2.492 80 271 1.092 .57 100 3140 9220 49 59 165 175 0 240 124 116 .327 232 108 3.054 .316 -1.611 -1.661
11 1493 401 224 171 1269 230 1483 389 211 198 1259 218 0 0 354 178 159 119 98 70 96 46 1499 1477 5.517 .181 .173 .154 .161 2.409 80 257 .429 .62 100 3280 9220 49 59 179 189 0 348 148 199 .157 337 189 6.361 .15 -2.669 -2.735
12 1034 1755 107 193 927 1562 1041 1765 217 221 934 1572 0 0 296 775 190 142 100 100 98 100 2489 2506 .593 1.685 1.683 1.521 1.622 1.498 52 146 2.115 .88 80 3410 9210 49 57 193 201 0 1522 167 1355 1.461 1531 1363 .684 1.46 .547 .546
13 650 543 199 206 451 337 643 474 212 245 444 268 0 0 259 325 159 226 90 57 71 27 788 712 1.338 .747 .604 .637 .695 2.17 120 359 1.272 .72 120 3540 9220 48 60 204 216 0 471 179 292 .648 411 232 1.543 .524 -.626 -.934
14 910 1307 355 257 555 1050 930 1114 334 281 575 857 0 0 246 643 141 139 94 100 88 94 1605 1432 .529 1.892 1.49 1.787 1.766 1.752 52 172 2.18 .85 80 3680 9210 49 57 220 228 0 1134 223 911 1.641 966 743 .609 1.293 .715 .37
15 1185 2542 393 277 792 2265 1088 2227 424 334 695 1950 0 0 482 1626 185 243 90 98 80 92 3057 2645 .35 2.86 2.806 2.559 2.838 2.074 52 223 3.245 .87 80 3800 9220 50 58 232 240 -100 2205 240 1965 2.48 1932 1691 .403 2.434 1.311 1.283
16 1640 1023 393 239 1247 784 1663 948 408 282 1270 709 0 0 297 370 151 216 100 100 100 86 2031 1979 1.591 .629 .558 .587 .583 1.512 52 280 .809 .83 90 3950 9210 48 57 246 255 0 887 207 680 .545 822 615 1.834 .484 -.875 -1.046
17 942 962 378 227 564 735 926 863 395 274 548 636 0 0 252 505 140 229 95 90 88 67 1299 1184 .767 1.303 1.161 1.19 1.223 2.07 80 291 1.747 .81 100 4090 9220 49 59 260 270 0 834 197 638 1.13 749 552 .885 1.007 .177 .01
18 640 822 350 290 290 532 559 483 466 471 209 193 0 0 404 1026 364 605 22 19 7 11 822 402 .545 1.834 .923 1.311 1.072 3.418 120 424 3.795 .67 120 4220 9220 48 60 272 284 -100 713 252 461 1.591 419 167 .628 .801 .67 -.32
19 532 634 317 234 215 400 515 573 341 298 198 339 0 0 115 252 171 455 57 42 15 1 615 537 .538 1.86 1.712 1.622 1.724 2.796 52 260 4.539 .52 90 4350 9210 48 57 286 295 0 550 203 347 1.614 497 294 .62 1.485 .69 .57
20 1531 1460 305 209 1226 1251 1490 1425 316 233 1185 1216 0 0 306 515 76 105 100 100 100 100 2477 2401 .98 1.02 1.026 .968 .988 1.399 52 235 1.214 .88 90 4510 9220 49 58 302 311 0 1266 181 1085 .885 1236 1055 1.13 .89 -.176 -.168

Total number of rows: 44544

Table truncated, full table size 9643 Kbytes.




Supplementary data files not provided
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