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Sample GSM88437 Query DataSets for GSM88437
Status Public on Dec 21, 2005
Title ARD531, CAIS, F, GOF, 6 x ETOH, 14d
Sample type RNA
 
Channel 1
Source name mixed reference (FR + CRG)
Organism Homo sapiens
Characteristics mixed reference (FR + CRG)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ARD531, G0, 6 x ETOH, 14 days
Organism Homo sapiens
Characteristics ARD531, G0, 6 x ETOH, 14 days
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17277.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
1 552 598 294 218 258 380 523 506 295 218 229 288 0 0 126 383 63 73 96 87 90 71 638 517 .679 1.473 1.258 1.046 1.195 3.147 32 170 2.736 .67 70 1510 9040 52 59 47 54 -100 820 299 521 2.02 694 395 .495 1.725 1.014 .786
2 381 433 292 216 89 217 319 222 297 218 27 6 0 0 211 538 65 65 30 27 20 20 306 33 .41 2.438 .222 1.462 1.55 3.694 120 393 3.603 .69 120 1630 9040 50 62 57 69 -100 594 296 298 3.344 304 8 .299 .305 1.742 -1.714
3 1532 874 293 177 1239 697 1527 818 296 183 1234 641 0 0 398 366 69 59 100 98 100 98 1936 1875 1.778 .563 .519 .519 .517 1.555 80 288 .716 .87 100 1760 9050 52 62 71 81 0 1199 243 956 .772 1122 879 1.296 .712 -.374 -.489
4 421 279 280 135 141 144 422 239 281 141 142 104 0 0 182 179 64 45 59 65 53 56 285 246 .979 1.021 .732 .907 .982 2.363 32 129 1.271 .7 60 1920 9060 55 61 89 95 0 383 185 197 1.401 328 143 .714 1.004 .486 .006
5 1175 2391 254 117 921 2274 1200 2470 257 121 946 2353 0 0 317 570 62 41 100 100 98 100 3195 3299 .405 2.469 2.487 2.556 2.477 1.659 80 383 2.67 .89 100 2040 9040 51 61 99 109 0 3279 160 3119 3.386 3388 3227 .295 3.411 1.76 1.77
6 440 256 238 92 202 164 422 189 243 95 184 97 0 0 189 149 57 28 75 81 59 65 366 281 1.232 .812 .527 .643 .695 2.007 32 115 1.037 .75 60 2190 9060 55 61 116 122 0 351 126 225 1.113 259 133 .898 .723 .155 -.468
7 910 431 245 95 665 336 906 442 250 102 661 347 0 0 175 114 56 44 100 96 100 96 1001 1008 1.979 .505 .525 .474 .514 1.751 80 278 .62 .85 100 2310 9050 52 62 126 136 0 591 130 461 .693 606 476 1.443 .72 -.529 -.474
8 1000 1935 245 95 755 1840 1018 2065 249 98 773 1970 0 0 204 575 56 30 100 98 100 98 2595 2743 .41 2.437 2.549 2.27 2.454 1.902 80 302 2.936 .86 100 2450 9040 51 61 140 150 0 2654 130 2524 3.342 2832 2702 .299 3.495 1.741 1.805
9 911 579 254 96 657 483 912 591 259 100 658 495 0 0 368 246 61 34 96 96 96 96 1140 1153 1.36 .735 .752 .709 .732 2.106 32 106 .908 .79 60 2590 9050 54 60 156 162 0 794 132 662 1.008 811 679 .992 1.032 .012 .045
10 291 116 254 103 37 13 282 107 263 107 28 4 0 0 72 41 63 33 33 28 13 10 50 32 2.846 .351 .143 .492 .486 4.063 120 426 9.143 .05 120 2710 9040 50 62 165 177 0 159 141 18 .482 147 5 2.075 .196 -1.053 -2.352
11 979 137 250 101 729 36 986 132 256 104 736 31 0 0 201 40 60 29 100 52 98 22 765 767 20.25 .049 .042 .057 .06 1.938 80 272 .241 .46 100 2860 9040 51 61 181 191 0 188 139 49 .068 181 43 14.765 .058 -3.884 -4.114
12 397 274 250 100 147 174 398 246 251 102 148 146 0 0 85 100 58 29 84 96 63 90 321 294 .845 1.184 .986 1.179 1.083 1.951 52 254 1.996 .56 90 2980 9040 51 60 193 202 0 376 137 239 1.623 337 200 .616 1.353 .699 .436
13 406 245 251 114 155 131 394 234 249 120 143 120 0 0 96 68 59 43 86 96 61 69 286 263 1.183 .845 .839 .874 .954 2.618 52 264 1.781 .46 90 3130 9050 52 61 208 217 0 336 156 180 1.159 321 165 .863 1.151 .213 .203
14 466 193 250 138 216 55 462 176 251 149 212 38 0 0 93 96 57 59 94 32 88 15 271 250 3.927 .255 .179 .275 .232 2.857 52 213 2.66 .23 90 3260 9040 51 60 221 230 0 265 189 75 .349 241 52 2.864 .246 -1.518 -2.024
15 277 227 261 173 16 54 270 195 267 179 9 22 0 0 71 122 63 55 20 30 5 16 70 31 .296 3.375 2.444 .989 1.248 5.576 120 452 5.701 .23 120 3390 9040 50 62 233 245 0 311 237 74 4.629 267 30 .216 3.353 2.211 1.745
16 456 612 287 217 169 395 425 452 289 221 138 235 0 0 213 383 60 52 65 93 53 84 564 373 .428 2.337 1.703 2.048 2.104 2.112 32 69 2.588 .71 60 3570 9000 49 55 254 260 -100 839 298 542 3.206 620 322 .312 2.335 1.681 1.224
17 275 205 267 142 8 63 273 175 272 153 6 33 0 0 64 96 64 56 15 37 3 20 71 39 .127 7.875 5.5 1.294 1.339 3.873 120 495 11.404 .11 120 3660 9040 50 62 260 272 0 281 195 86 10.8 240 45 .093 7.543 3.433 2.915
18 376 168 267 112 109 56 382 161 259 110 115 49 0 0 91 42 59 28 65 75 50 37 165 164 1.946 .514 .426 .468 .508 2.391 32 155 1.557 .33 70 3800 9050 53 60 276 283 0 230 154 77 .705 221 67 1.419 .584 -.505 -.775
19 371 366 256 107 115 259 380 374 259 108 124 267 0 0 84 82 60 30 73 98 51 98 374 391 .444 2.252 2.153 2.358 2.38 1.994 80 303 2.568 .58 100 3940 9040 51 61 289 299 0 502 147 355 3.089 513 366 .324 2.953 1.627 1.562
20 870 675 257 105 613 570 879 664 261 107 622 559 0 0 237 126 57 29 92 100 92 100 1183 1181 1.075 .93 .899 1.034 .889 2.132 80 217 .981 .87 100 4080 9050 52 62 303 313 0 926 144 782 1.275 911 767 .784 1.233 .351 .302

Total number of rows: 44544

Table truncated, full table size 9425 Kbytes.




Supplementary data files not provided
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