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Sample GSM88434 Query DataSets for GSM88434
Status Public on Dec 21, 2005
Title N-56, NORM, M, GSF, 6 x 100nM DHT, 14d
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, 14 days DMEM F12 12.9% D/S FCS + 6 x 100nM DHT
Organism Homo sapiens
Characteristics nGSF56, 14 days DMEM F12 12.9% D/S FCS + 6 x 100nM DHT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15582.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
1 473 326 298 159 175 167 473 329 306 167 175 170 0 0 82 91 67 65 90 84 68 68 342 345 1.048 .954 .971 .9 .946 2.431 32 216 2.121 .51 70 1910 9180 54 61 47 54 0 301 147 154 .88 303 157 1.136 .896 -.184 -.158
2 566 372 329 164 237 208 545 330 332 170 216 166 0 0 245 221 68 65 71 68 59 56 445 382 1.139 .878 .769 .896 .876 2.215 32 168 1.285 .73 70 2060 9190 55 62 62 69 0 343 151 192 .81 304 153 1.235 .709 -.305 -.496
3 1949 1464 398 206 1551 1258 1973 1496 402 219 1575 1290 0 0 412 466 91 97 100 100 100 98 2809 2865 1.233 .811 .819 .77 .795 1.575 80 321 .928 .91 100 2190 9180 53 63 74 84 0 1350 190 1160 .748 1380 1190 1.337 .755 -.419 -.405
4 551 400 377 184 174 216 497 393 377 189 120 209 0 0 215 235 71 75 50 68 50 53 390 329 .806 1.241 1.742 1.744 1.405 3.159 32 137 1.554 .7 70 2330 9190 55 62 89 96 0 369 170 199 1.145 362 193 .873 1.606 .195 .684
5 1333 2140 387 215 946 1925 1337 2157 399 223 950 1942 0 0 270 595 94 109 100 100 98 97 2871 2892 .491 2.035 2.044 1.991 2.055 1.443 80 338 2.199 .9 100 2450 9170 52 62 100 110 0 1974 198 1776 1.877 1990 1791 .533 1.886 .908 .915
6 590 344 348 166 242 178 544 278 355 176 196 112 0 0 181 171 75 80 81 59 68 43 420 308 1.36 .736 .571 .602 .569 2.141 32 157 1.369 .64 70 2600 9190 55 62 116 123 0 317 153 164 .678 256 103 1.474 .527 -.56 -.924
7 1376 1746 365 181 1011 1565 1386 1744 368 191 1021 1563 0 0 315 550 73 80 100 100 100 100 2576 2584 .646 1.548 1.531 1.511 1.596 1.43 80 346 1.704 .92 110 2730 9170 51 62 127 138 0 1610 167 1444 1.428 1609 1442 .7 1.412 .514 .498
8 1447 1052 392 184 1055 868 1437 1036 392 195 1045 852 0 0 288 260 77 78 100 100 100 98 1923 1897 1.215 .823 .815 .809 .828 1.316 80 322 .933 .9 100 2860 9170 52 62 141 151 0 970 170 801 .759 956 786 1.318 .752 -.398 -.411
9 1318 766 390 182 928 584 1227 762 394 188 837 580 0 0 316 239 82 79 100 96 100 96 1512 1417 1.589 .629 .693 .562 .633 2.129 32 163 .978 .7 60 3020 9170 54 60 159 165 0 707 168 539 .58 703 535 1.723 .639 -.785 -.646
10 560 408 430 210 130 198 558 341 437 228 128 131 0 0 154 182 93 95 56 71 34 43 328 259 .657 1.523 1.023 1.396 1.316 2.862 32 131 3.445 .34 60 3150 9160 53 59 172 178 0 376 194 183 1.405 315 121 .712 .944 .49 -.083
11 1461 342 447 223 1014 119 1460 309 450 238 1013 86 0 0 337 115 93 98 100 48 100 20 1133 1099 8.521 .117 .085 .106 .131 2.477 80 279 .476 .46 100 3270 9160 51 61 182 192 0 315 206 110 .108 285 79 9.238 .078 -3.208 -3.675
12 1012 1304 387 181 625 1123 1020 1282 396 189 633 1101 0 0 207 378 86 68 100 100 98 100 1748 1734 .557 1.797 1.739 1.791 1.824 1.457 80 256 2.073 .89 100 3410 9170 52 62 196 206 0 1203 167 1036 1.657 1183 1016 .603 1.604 .729 .682
13 667 453 384 199 283 254 669 436 388 203 285 237 0 0 122 149 81 69 96 92 83 75 537 522 1.114 .898 .832 .822 .891 2.499 80 258 1.595 .65 100 3540 9170 52 62 209 219 0 418 184 234 .828 402 219 1.208 .767 -.273 -.383
14 641 494 366 195 275 299 652 463 364 201 286 268 0 0 111 146 68 73 95 95 87 86 574 554 .92 1.087 .937 1.062 1.028 2.349 80 279 1.706 .67 100 3680 9170 52 62 223 233 0 456 180 276 1.003 427 247 .997 .864 .004 -.21
15 780 832 360 161 420 671 750 820 363 175 390 659 0 0 189 263 72 73 100 100 96 100 1091 1049 .626 1.598 1.69 1.642 1.518 1.533 52 203 1.827 .81 80 3800 9170 53 61 236 244 0 767 149 619 1.474 756 608 .679 1.559 .559 .64
16 1054 547 381 161 673 386 1082 563 382 177 701 402 0 0 213 176 75 71 97 95 97 90 1059 1103 1.744 .574 .573 .521 .577 1.915 80 293 .753 .83 100 3950 9160 51 61 250 260 0 505 149 356 .529 519 371 1.89 .529 -.919 -.919
17 610 386 350 147 260 239 621 386 355 161 271 239 0 0 120 126 76 85 94 94 80 65 499 510 1.088 .919 .882 .937 .944 1.991 52 227 1.645 .6 90 4080 9170 52 61 263 272 0 356 136 220 .848 356 220 1.179 .813 -.238 -.298
18 438 258 327 142 111 116 443 250 328 155 116 108 0 0 64 86 63 85 73 67 38 19 227 224 .957 1.045 .931 1.134 1.187 2.784 52 233 2.882 .36 80 4210 9170 53 61 277 285 0 238 131 107 .964 231 100 1.037 .859 -.053 -.22
19 443 235 338 154 105 81 438 211 337 167 100 57 0 0 105 91 67 70 59 40 37 25 186 157 1.296 .771 .57 .79 .898 5.412 32 144 3.334 .28 60 4350 9150 52 58 292 298 0 217 142 75 .712 195 53 1.405 .526 -.491 -.928
20 1184 830 331 141 853 689 1175 833 338 158 844 692 0 0 197 269 67 76 100 98 100 98 1542 1536 1.238 .808 .82 .754 .834 1.609 52 245 1.029 .86 90 4480 9160 51 60 303 312 0 766 130 636 .745 768 638 1.342 .756 -.425 -.403

Total number of rows: 44544

Table truncated, full table size 9589 Kbytes.




Supplementary data files not provided
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