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Sample GSM88433 Query DataSets for GSM88433
Status Public on Dec 21, 2005
Title ARD531, 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 ARD531, G0, 6 x 100nM DHT, 14 days
Organism Homo sapiens
Characteristics ARD531, 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/2001-06/17291.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
1 292 139 213 53 79 86 284 145 213 55 71 92 0 0 63 32 48 22 65 100 40 87 165 163 .919 1.089 1.296 1.191 .92 3.011 32 152 2.699 .32 60 1310 9090 50 56 44 50 0 141 54 88 1.108 148 94 .902 1.319 .148 .399
2 362 800 218 53 144 747 339 846 216 56 121 793 0 0 141 432 47 21 65 96 53 96 891 914 .193 5.188 6.554 4.479 3.923 2.335 32 108 5.217 .7 60 1440 9100 51 57 57 63 0 814 54 760 5.281 861 807 .189 6.671 2.401 2.738
3 779 462 213 49 566 413 786 467 214 53 573 418 0 0 213 96 44 20 97 100 95 100 979 991 1.37 .73 .729 .782 .725 1.844 80 318 .776 .87 100 1560 9080 47 57 67 77 0 470 50 420 .743 475 426 1.346 .743 -.429 -.429
4 284 94 213 49 71 45 267 95 210 52 54 46 0 0 126 48 39 19 56 62 40 53 116 100 1.578 .634 .852 .382 .411 3.339 32 138 .86 .49 60 1710 9080 49 55 84 90 0 96 50 46 .645 97 47 1.55 .867 -.632 -.206
5 935 2321 214 52 721 2269 973 2403 217 54 759 2351 0 0 240 407 63 19 93 100 93 100 2990 3110 .318 3.147 3.097 3.226 3.055 1.612 80 389 3.248 .91 100 1840 9070 46 56 95 105 0 2363 53 2310 3.203 2446 2393 .312 3.153 1.68 1.657
6 409 157 191 51 218 106 425 142 195 54 234 91 0 0 160 101 45 18 81 78 71 65 324 325 2.057 .486 .389 .426 .399 3.125 32 177 .838 .67 70 1990 9080 48 55 111 118 0 160 52 108 .495 145 93 2.02 .396 -1.015 -1.337
7 747 387 201 49 546 338 766 418 204 53 565 369 0 0 175 128 45 18 98 97 98 96 884 934 1.615 .619 .653 .581 .616 1.662 80 288 .77 .84 100 2120 9060 45 55 123 133 0 394 50 344 .63 426 376 1.587 .665 -.666 -.589
8 792 1885 212 50 580 1835 832 1891 212 54 620 1841 0 0 217 341 43 18 95 100 93 100 2415 2461 .316 3.164 2.969 3.296 3.041 1.667 80 284 3.271 .88 100 2240 9070 46 56 135 145 0 1919 51 1868 3.221 1925 1874 .311 3.023 1.687 1.596
9 778 455 214 52 564 403 777 484 216 55 563 432 0 0 297 222 48 19 100 90 93 87 967 995 1.4 .715 .767 .581 .68 2.066 32 201 .883 .82 70 2390 9070 47 54 151 158 0 463 53 410 .727 493 440 1.375 .781 -.459 -.356
10 284 88 224 56 60 32 286 82 223 57 62 26 0 0 42 27 50 21 68 59 18 31 92 88 1.875 .533 .419 .458 .463 3.005 32 176 1.709 .29 70 2530 9060 46 53 165 172 0 90 57 33 .543 83 26 1.842 .427 -.881 -1.228
11 918 127 212 60 706 67 909 122 212 65 697 62 0 0 132 38 48 29 100 86 100 57 773 759 10.537 .095 .089 .091 .094 1.721 52 314 .206 .67 90 2650 9060 45 54 176 185 0 129 61 68 .097 124 63 10.352 .091 -3.372 -3.465
12 324 345 209 63 115 282 312 320 211 90 103 257 0 0 72 128 47 82 81 100 50 78 397 360 .408 2.452 2.495 2.536 2.55 1.854 32 177 3.153 .68 70 2780 9050 45 52 190 197 0 351 64 287 2.496 326 262 .401 2.54 1.32 1.345
13 364 249 206 74 158 175 360 229 209 88 154 155 0 0 82 108 47 61 95 95 76 73 333 309 .903 1.108 1.006 1.043 1.074 2.125 80 303 2.228 .53 100 2930 9070 46 56 204 214 0 253 75 178 1.127 233 158 .887 1.025 .173 .035
14 406 206 218 79 188 127 400 196 221 86 182 117 0 0 90 55 45 38 93 100 85 82 315 299 1.48 .676 .643 .71 .643 2.114 80 220 1.185 .57 100 3060 9070 46 56 217 227 0 210 80 129 .688 200 119 1.454 .654 -.54 -.612
15 237 86 226 84 11 2 235 80 230 91 9 -4 0 0 50 35 49 37 21 10 5 3 13 5 5.5 .182 null .622 .667 3.36 120 301 6.382 .12 120 3190 9070 45 57 229 241 0 88 86 2 .185 81 -4 5.403 null -2.434 null
16 268 112 224 78 44 34 247 90 228 83 23 12 0 0 100 106 49 30 39 26 12 13 78 35 1.294 .773 .522 .676 .667 4.31 120 308 2.041 .57 120 3320 9070 45 57 242 254 0 114 79 35 .787 92 12 1.271 .531 -.346 -.913
17 233 104 213 71 20 33 235 87 215 75 22 16 0 0 48 65 45 25 32 35 7 18 53 38 .606 1.65 .727 .753 .602 3.859 120 358 6.989 .14 120 3460 9070 45 57 256 268 0 106 72 34 1.68 89 16 .595 .74 .748 -.434
18 322 160 218 67 104 93 318 155 221 71 100 88 0 0 71 43 51 26 71 96 50 82 197 188 1.118 .894 .88 .904 .988 2.539 52 204 1.429 .48 80 3610 9070 47 55 273 281 0 163 68 95 .91 158 90 1.099 .896 -.136 -.159
19 350 331 224 63 126 268 357 325 229 68 133 262 0 0 68 62 50 25 88 100 63 100 394 395 .47 2.127 1.97 2.347 1.922 2.044 52 252 2.766 .63 90 3750 9060 45 54 286 295 0 337 64 273 2.165 331 267 .462 2.005 1.114 1.004
20 744 688 218 60 526 628 752 702 223 61 534 642 0 0 128 153 48 19 98 100 98 98 1154 1176 .838 1.194 1.202 1.181 1.229 1.317 80 241 1.36 .89 100 3880 9060 45 55 299 309 0 700 61 639 1.215 715 654 .823 1.224 .281 .291

Total number of rows: 44544

Table truncated, full table size 9351 Kbytes.




Supplementary data files not provided
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