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Sample GSM88439 Query DataSets for GSM88439
Status Public on Dec 21, 2005
Title ARD842, CAIS, F, GOF, 1 x 1000nM DHT, 24h
Sample type RNA
 
Channel 1
Source name mixed reference (MR = CRG + FR)
Organism Homo sapiens
Characteristics mixed reference (MR = CRG + FR)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ARD842, CAIS, proliferating cells, 24h 1000nM DHT
Organism Homo sapiens
Characteristics ARD842, CAIS, proliferating cells, 24h 1000nM DHT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16834.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) [email protected]
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
1 585 307 425 203 160 104 553 268 425 212 128 65 0 0 111 133 82 79 78 46 38 28 264 193 1.538 .65 .508 .581 .693 3.457 52 246 3.918 .25 80 1740 9640 48 56 70 78 0 311 206 105 .659 272 66 1.517 .515 -.602 -.958
2 756 1003 418 181 338 822 725 947 423 194 307 766 0 0 311 356 91 66 68 100 59 100 1160 1073 .411 2.432 2.495 3.078 2.172 3.13 32 139 2.244 .72 60 1860 9640 49 55 83 89 0 1017 184 833 2.466 960 777 .406 2.53 1.302 1.339
3 2273 1923 439 174 1834 1749 2372 1888 442 184 1933 1714 0 0 407 302 80 60 100 100 98 100 3583 3647 1.049 .954 .887 .982 .954 1.45 80 291 1.001 .92 100 2020 9630 46 56 97 107 0 1950 176 1773 .967 1914 1738 1.034 .899 -.049 -.154
4 500 184 443 159 57 25 452 164 446 163 9 5 0 0 187 99 84 52 27 24 16 15 82 14 2.28 .439 .556 .558 .538 4.3 120 357 1.48 .38 120 2150 9630 45 57 109 121 0 187 161 25 .445 166 5 2.249 .563 -1.169 -.828
5 1789 4810 441 147 1348 4663 1769 4922 445 149 1328 4775 0 0 241 757 93 50 100 100 100 100 6011 6103 .289 3.459 3.596 3.458 3.59 1.302 80 315 3.821 .91 110 2300 9630 45 56 124 135 0 4877 149 4728 3.507 4990 4841 .285 3.645 1.81 1.866
6 470 192 444 143 26 49 452 158 446 146 8 15 0 0 140 109 92 48 25 32 13 20 75 23 .531 1.885 1.875 .55 .61 3.81 120 399 1.558 .45 120 2420 9630 45 57 136 148 0 195 145 50 1.911 160 15 .523 1.901 .934 .927
7 1598 663 446 142 1152 521 1586 685 446 146 1140 543 0 0 281 184 80 49 100 100 98 98 1673 1683 2.211 .452 .476 .434 .456 1.542 80 249 .558 .86 100 2570 9630 46 56 152 162 0 672 144 528 .459 694 551 2.181 .483 -1.125 -1.05
8 2175 4537 432 145 1743 4392 2195 4539 436 146 1763 4394 0 0 400 767 87 47 100 100 100 100 6135 6157 .397 2.52 2.492 2.549 2.521 1.323 80 276 2.738 .9 110 2700 9630 45 56 164 175 0 4600 147 4453 2.555 4602 4455 .391 2.527 1.353 1.337
9 1037 1594 440 142 597 1452 1016 1612 437 151 576 1470 0 0 348 842 92 62 88 100 88 98 2049 2046 .411 2.432 2.552 2.383 2.395 1.967 52 130 2.974 .79 80 2820 9640 48 56 178 186 0 1616 144 1472 2.466 1634 1490 .406 2.587 1.302 1.372
10 477 141 419 133 58 8 475 138 426 143 56 5 0 0 98 48 90 58 37 12 10 5 66 61 7.25 .138 .089 .371 .294 4.557 120 348 13.216 .04 120 2960 9630 45 57 190 202 0 143 135 8 .14 140 5 7.151 .091 -2.838 -3.466
11 1440 204 429 136 1011 68 1424 189 435 137 995 53 0 0 255 74 88 47 100 55 100 35 1079 1048 14.868 .067 .053 .072 .075 2.372 80 227 .705 .29 100 3110 9630 46 56 206 216 0 207 138 69 .068 192 54 14.665 .054 -3.874 -4.211
12 540 495 431 140 109 355 528 379 437 152 97 239 0 0 108 392 87 98 53 90 25 60 464 336 .307 3.257 2.464 2.758 2.597 3.584 80 261 13.747 .21 100 3240 9630 46 56 219 229 -100 502 142 360 3.302 384 242 .303 2.498 1.723 1.321
13 715 400 426 140 289 260 724 391 428 147 298 251 0 0 141 113 87 74 93 98 80 85 549 549 1.112 .9 .842 .961 .852 2.643 80 292 1.636 .53 100 3380 9630 46 56 233 243 0 406 142 264 .912 396 254 1.096 .854 -.133 -.228
14 689 399 422 144 267 255 709 400 431 165 287 256 0 0 140 109 115 172 86 80 66 17 522 543 1.047 .955 .892 .967 .881 2.31 80 285 1.372 .56 110 3530 9620 44 55 247 258 0 405 146 259 .968 406 260 1.033 .904 -.047 -.145
15 440 209 424 150 16 59 438 178 432 164 14 28 0 0 101 98 110 156 14 14 2 3 75 42 .271 3.688 2 .617 .662 3.258 120 358 5.529 .15 120 3640 9630 45 57 258 270 0 212 152 60 3.739 180 28 .267 2.028 1.902 1.02
16 1106 556 429 139 677 417 1158 546 428 140 729 407 0 0 596 331 87 44 75 84 65 78 1094 1136 1.624 .616 .558 .495 .638 2.437 32 125 .684 .84 60 3790 9620 47 53 276 282 0 564 141 423 .624 554 413 1.601 .566 -.679 -.821
17 808 605 411 136 397 469 774 596 412 138 363 460 0 0 195 120 80 43 97 100 92 98 866 823 .846 1.181 1.267 1.218 1.125 1.622 80 370 1.357 .73 110 3930 9620 44 55 287 298 0 613 138 475 1.198 604 466 .835 1.285 .26 .362
18 591 156 412 131 179 25 602 158 417 132 190 27 0 0 114 37 87 42 75 38 55 5 204 217 7.16 .14 .142 .263 .27 2.827 52 198 8.335 .04 80 4070 9630 47 55 303 311 0 158 133 25 .142 160 27 7.062 .144 -2.82 -2.795
19 635 443 415 128 220 315 613 449 422 132 198 321 0 0 142 91 84 41 83 100 58 98 535 519 .698 1.432 1.621 1.719 1.423 2.237 80 321 1.754 .62 110 4210 9620 44 55 315 326 0 449 130 319 1.452 455 325 .689 1.644 .538 .717
20 1524 1409 425 131 1099 1278 1534 1381 437 135 1109 1250 0 0 327 237 86 43 98 100 98 100 2377 2359 .86 1.163 1.127 1.19 1.137 1.372 80 260 1.246 .87 110 4340 9620 44 55 328 339 0 1429 133 1296 1.179 1400 1267 .848 1.143 .238 .193

Total number of rows: 44544

Table truncated, full table size 9660 Kbytes.




Supplementary data files not provided
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