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Sample GSM88441 Query DataSets for GSM88441
Status Public on Dec 21, 2005
Title N-56, NORM, M, GSF, 1 x 1000nM DHT, 24h
Sample type RNA
 
Channel 1
Source name mixed reference
Organism Homo sapiens
Characteristics mixed reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name nGSF56, proliferating cells, 24h 1000nM DHT
Organism Homo sapiens
Characteristics nGSF56, proliferating cells, 24h 1000nM DHT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16686.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
1 545 366 294 99 251 267 543 354 294 103 249 255 0 0 134 106 55 37 92 100 90 97 518 504 .94 1.064 1.024 1.064 .997 1.958 80 328 1.404 .68 100 1620 9180 61 71 57 67 0 446 121 326 1.298 432 311 .771 1.249 .376 .321
2 366 291 287 102 79 189 283 138 287 106 -4 36 0 0 243 345 59 37 30 49 22 38 268 32 .418 2.392 null 1.058 1.119 3.87 120 346 1.839 .78 120 1750 9170 59 71 69 81 -100 355 124 231 2.918 168 44 .343 null 1.545 null
3 1881 1498 271 100 1610 1398 1943 1558 276 109 1672 1458 0 0 514 432 60 50 98 100 98 100 3008 3130 1.152 .868 .872 .895 .867 1.456 80 267 .903 .95 110 1900 9170 59 70 84 95 0 1827 122 1705 1.059 1900 1778 .944 1.064 .083 .089
4 329 159 279 97 50 62 272 114 282 106 -7 17 0 0 203 130 63 55 20 30 15 13 112 10 .806 1.24 null .789 .695 3.686 120 338 .972 .72 120 2020 9170 59 71 96 108 -100 194 118 76 1.513 139 21 .661 null .597 null
5 1797 2121 298 104 1499 2017 1823 2138 301 115 1525 2034 0 0 374 401 64 137 100 100 100 100 3516 3559 .743 1.346 1.334 1.369 1.322 1.273 80 261 1.385 .95 110 2150 9170 59 70 109 120 0 2587 127 2460 1.641 2608 2481 .609 1.627 .715 .702
6 348 264 275 103 73 161 295 142 285 117 20 39 0 0 186 344 74 123 30 26 19 15 234 59 .453 2.205 1.95 1.04 1.012 3.119 120 377 2.673 .78 120 2290 9170 59 71 123 135 -100 322 126 196 2.69 173 48 .372 2.379 1.428 1.25
7 1555 1282 270 98 1285 1184 1597 1301 274 105 1327 1203 0 0 325 284 54 43 100 100 100 100 2469 2530 1.085 .921 .907 .923 .895 1.298 80 265 .951 .96 100 2430 9160 59 69 138 148 0 1564 120 1444 1.124 1587 1467 .89 1.106 .169 .145
8 1534 1357 277 107 1257 1250 1583 1404 277 115 1306 1297 0 0 392 328 62 44 98 100 98 100 2507 2603 1.006 .994 .993 1.03 .975 1.394 80 262 1.009 .94 100 2560 9160 59 69 151 161 0 1655 131 1525 1.213 1713 1582 .824 1.211 .279 .277
9 1051 1375 284 102 767 1273 1006 1417 282 110 722 1315 0 0 494 562 61 41 92 100 86 98 2040 2037 .603 1.66 1.821 1.977 1.752 2.041 52 199 1.609 .91 80 2690 9150 59 67 165 173 0 1677 124 1553 2.024 1728 1604 .494 2.222 1.018 1.152
10 524 177 288 106 236 71 514 171 286 112 226 65 0 0 115 63 59 41 95 70 86 35 307 291 3.324 .301 .288 .298 .333 3.607 80 295 .934 .48 100 2830 9170 60 70 178 188 0 216 129 87 .367 209 79 2.725 .351 -1.446 -1.511
11 1414 203 281 105 1133 98 1467 202 285 123 1186 97 0 0 288 63 57 134 100 23 100 0 1231 1283 11.561 .086 .082 .083 .086 1.99 80 264 .181 .64 100 2970 9160 59 69 192 202 0 248 128 120 .106 246 118 9.478 .1 -3.245 -3.325
12 591 519 283 100 308 419 594 499 287 109 311 399 0 0 164 171 59 43 91 100 87 100 727 710 .735 1.36 1.283 1.373 1.33 1.997 80 274 1.694 .76 110 3100 9170 59 70 204 215 0 633 122 511 1.659 609 487 .603 1.565 .731 .646
13 797 507 297 104 500 403 824 504 301 110 527 400 0 0 201 131 67 41 96 100 93 100 903 927 1.241 .806 .759 .872 .832 1.761 80 275 .885 .86 100 3240 9170 60 70 219 229 0 618 127 492 .983 615 488 1.017 .926 -.025 -.111
14 751 479 287 110 464 369 750 466 289 120 463 356 0 0 120 136 65 50 100 100 98 100 833 819 1.257 .795 .769 .771 .75 1.506 80 373 1.068 .82 110 3390 9160 58 69 233 244 0 584 134 450 .97 568 434 1.031 .938 -.044 -.093
15 457 412 284 110 173 302 411 276 305 138 127 166 0 0 200 361 149 116 43 56 28 40 475 293 .573 1.746 1.307 1.138 1.338 2.696 32 182 1.896 .82 70 3510 9150 59 66 247 254 -100 503 134 368 2.129 337 202 .47 1.594 1.09 .673
16 1157 748 285 117 872 631 1212 793 319 146 927 676 0 0 417 247 183 123 87 90 87 87 1503 1603 1.382 .724 .729 .762 .721 1.51 32 195 .759 .93 70 3650 9150 59 66 261 268 0 912 143 770 .883 967 825 1.133 .889 -.18 -.169
17 803 718 265 115 538 603 807 717 275 127 542 602 0 0 153 153 104 70 100 100 100 100 1141 1144 .892 1.121 1.111 1.131 1.136 1.394 80 332 1.309 .85 110 3790 9170 59 70 273 284 0 876 140 736 1.367 875 734 .731 1.355 .451 .438
18 525 209 256 118 269 91 521 207 260 125 265 89 0 0 85 57 57 54 100 73 98 30 360 354 2.956 .338 .336 .304 .337 2.176 80 289 .994 .5 100 3930 9160 59 69 288 298 0 255 144 111 .413 252 109 2.423 .41 -1.277 -1.288
19 602 401 259 112 343 289 579 265 259 119 320 153 0 0 194 432 55 50 92 85 90 75 632 473 1.187 .843 .478 .555 .509 2.86 80 301 2.028 .7 100 4060 9150 58 68 301 311 0 489 137 353 1.028 323 187 .973 .583 .039 -.778
20 1305 941 271 119 1034 822 1304 920 269 124 1033 801 0 0 262 219 53 47 100 100 100 100 1856 1834 1.258 .795 .775 .794 .773 1.305 80 272 .853 .93 100 4200 9160 59 69 315 325 0 1148 145 1003 .97 1122 977 1.031 .946 -.044 -.08

Total number of rows: 44544

Table truncated, full table size 9675 Kbytes.




Supplementary data files not provided
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