NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88464 Query DataSets for GSM88464
Status Public on Dec 21, 2005
Title ARD402, CAIS, F, GSF
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 ARD 402 14 days DMEM F12, 12.9% FCS, Go, against mied reference
Organism Homo sapiens
Characteristics ARD 402 14 days DMEM F12, 12.9% FCS, Go, against mied reference
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16449.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 GPL3266
Series (2)
GSE3872 Baseline gene transcription in 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
1 673 549 257 252 416 297 639 508 264 259 382 256 0 0 185 204 71 100 98 85 96 66 713 638 1.401 .714 .67 .637 .702 1.704 80 406 1.089 .81 100 1490 9260 61 71 28 38 0 675 310 365 .877 624 315 1.14 .824 -.189 -.28
2 659 1086 257 251 402 835 673 1115 265 253 416 864 0 0 223 197 65 57 91 100 91 100 1237 1280 .481 2.077 2.077 2.437 2.006 2.008 12 99 2.365 .75 50 1630 9260 63 68 44 49 0 1335 308 1026 2.553 1370 1062 .392 2.553 1.352 1.352
3 2390 1477 257 248 2133 1229 2142 1439 258 254 1885 1191 0 0 1064 700 56 51 100 93 100 92 3362 3076 1.736 .576 .632 .516 .557 1.802 80 310 .676 .9 100 1760 9250 60 70 55 65 0 1815 305 1510 .708 1769 1464 1.412 .777 -.498 -.365
4 314 310 264 258 50 52 287 287 274 260 23 29 0 0 112 113 76 59 25 33 13 17 102 52 .962 1.04 1.261 .984 1.159 3.531 80 280 2.52 .39 100 1890 9250 60 70 68 78 0 381 317 64 1.278 353 36 .782 1.55 .354 .632
5 1605 844 260 258 1345 586 1670 903 263 261 1410 645 0 0 486 295 64 61 97 90 97 87 1931 2055 2.295 .436 .457 .372 .462 2.126 80 267 .552 .88 100 2030 9250 60 70 82 92 0 1037 317 720 .535 1110 793 1.868 .562 -.901 -.831
6 348 417 257 264 91 153 282 304 261 266 25 40 0 0 192 360 59 57 40 40 23 25 244 65 .595 1.681 1.6 1.09 1.048 3.835 80 254 2.43 .73 100 2170 9250 60 70 96 106 0 513 324 188 2.066 374 49 .484 1.966 1.047 .976
7 1475 805 261 259 1214 546 1448 822 267 265 1187 563 0 0 475 238 56 53 100 97 100 96 1760 1750 2.223 .45 .474 .442 .456 1.444 80 247 .525 .9 100 2300 9250 60 70 109 119 0 989 318 671 .553 1010 692 1.809 .583 -.855 -.779
8 1941 1452 276 247 1665 1205 1859 1461 279 256 1583 1214 0 0 646 533 70 59 100 98 100 98 2870 2797 1.382 .724 .767 .704 .71 1.483 80 276 .828 .9 100 2440 9250 60 70 123 133 0 1785 304 1481 .889 1796 1492 1.124 .943 -.169 -.085
9 1587 1190 296 261 1291 929 1581 1219 301 267 1285 958 0 0 827 523 75 62 94 98 92 96 2220 2243 1.39 .72 .746 .802 .721 2.044 52 211 .777 .88 80 2590 9260 62 70 139 147 0 1463 321 1142 .884 1498 1177 1.131 .916 -.177 -.126
10 637 556 291 250 346 306 596 474 302 255 305 224 0 0 198 264 70 53 100 90 88 84 652 529 1.131 .884 .734 .773 1.025 2.384 52 179 1.453 .74 80 2730 9260 62 70 153 161 0 683 307 376 1.087 583 275 .92 .903 .12 -.148
11 1812 420 287 249 1525 171 1766 391 290 257 1479 142 0 0 734 191 72 58 100 61 100 55 1696 1621 8.918 .112 .096 .106 .11 2.276 80 266 .269 .66 100 2850 9250 60 70 164 174 0 516 306 210 .138 481 175 7.256 .118 -2.859 -3.083
12 1250 1418 283 260 967 1158 1248 1273 289 268 965 1013 0 0 492 714 65 58 98 100 98 98 2125 1978 .835 1.198 1.05 1.15 1.331 1.924 52 205 1.456 .86 80 2980 9250 61 69 178 186 0 1743 320 1423 1.472 1565 1245 .679 1.29 .558 .368
13 793 766 306 280 487 486 762 747 312 294 456 467 0 0 206 163 82 82 96 100 94 98 973 923 1.002 .998 1.024 1.049 .977 1.758 52 275 1.134 .81 90 3130 9250 60 69 192 201 0 941 344 597 1.227 918 574 .815 1.259 .295 .332
14 1172 1384 329 319 843 1065 1102 1287 344 339 773 968 0 0 364 551 95 108 100 100 98 98 1908 1741 .792 1.263 1.252 1.224 1.248 1.544 52 267 1.439 .87 90 3270 9240 59 68 206 215 0 1701 392 1309 1.553 1582 1190 .644 1.539 .635 .622
15 1642 2500 315 302 1327 2198 1650 2288 327 315 1335 1986 0 0 786 1477 92 87 92 96 90 92 3525 3321 .604 1.656 1.488 1.583 1.669 2.412 80 288 1.854 .93 100 3410 9250 60 70 220 230 0 3073 371 2701 2.036 2812 2441 .491 1.828 1.026 .871
16 1496 925 305 298 1191 627 1499 933 314 303 1194 635 0 0 289 193 73 65 100 100 100 100 1818 1829 1.9 .526 .532 .515 .515 1.357 80 335 .601 .91 110 3550 9250 59 70 233 244 0 1137 366 771 .647 1147 780 1.546 .654 -.628 -.613
17 1338 1357 342 345 996 1012 1344 1359 350 365 1002 1014 0 0 372 392 82 102 100 100 100 100 2008 2016 .984 1.016 1.012 1.029 1.092 1.515 52 256 1.176 .87 90 3690 9240 59 68 248 257 0 1668 424 1244 1.249 1670 1246 .801 1.244 .321 .315
18 682 693 357 377 325 316 692 680 362 391 335 303 0 0 134 200 79 123 97 88 86 67 641 638 1.028 .972 .904 .861 .923 2.247 80 318 1.663 .67 100 3830 9250 60 70 262 272 0 852 463 388 1.195 836 372 .837 1.112 .257 .153
19 760 578 329 284 431 294 754 542 337 291 425 258 0 0 185 190 77 66 98 92 94 82 725 683 1.466 .682 .607 .629 .664 2.561 52 187 1.161 .69 80 3980 9260 62 70 278 286 0 710 349 361 .838 666 317 1.193 .746 -.254 -.423
20 1244 1227 335 305 909 922 1229 1161 345 308 894 856 0 0 265 318 82 74 100 100 100 100 1831 1750 .986 1.014 .957 1 1.058 1.431 52 207 1.164 .88 90 4090 9250 60 69 288 297 0 1508 375 1133 1.247 1427 1052 .802 1.177 .318 .235

Total number of rows: 43392

Table truncated, full table size 9468 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap