NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88423 Query DataSets for GSM88423
Status Public on Dec 21, 2005
Title N-58, NORM, M, GSF, 1 x 1000nM DHT, 24h
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 nGSF58, 24h 1000nM DHT
Organism Homo sapiens
Characteristics nGSF58, 24h 1000nM DHT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16893.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
1 536 459 385 125 151 334 514 284 390 135 129 159 0 0 115 368 74 58 65 81 43 59 485 288 .452 2.212 1.233 1.518 1.808 3.232 32 178 4.409 .49 70 1700 9650 53 60 42 49 0 401 109 292 1.932 248 139 .518 1.076 .95 .106
2 598 465 354 90 244 375 579 448 354 93 225 358 0 0 192 186 65 30 78 100 68 100 619 583 .651 1.537 1.591 1.769 1.428 2.326 32 134 1.618 .75 60 1820 9640 53 59 55 61 0 406 79 328 1.342 391 313 .745 1.39 .425 .475
3 1728 1458 349 90 1379 1368 1795 1448 353 94 1446 1358 0 0 367 290 69 32 100 100 100 100 2747 2804 1.008 .992 .939 1.013 .958 1.268 80 395 1.029 .95 110 1970 9620 48 59 67 78 0 1273 79 1195 .866 1265 1186 1.154 .82 -.207 -.286
4 623 379 346 83 277 296 533 292 349 87 187 209 0 0 249 285 68 32 81 84 65 78 573 396 .936 1.069 1.118 .902 .802 2.666 32 131 1.441 .73 60 2100 9630 52 58 83 89 0 331 72 259 .933 255 183 1.071 .976 -.1 -.035
5 2025 3094 344 84 1681 3010 2061 3071 347 90 1717 2987 0 0 276 454 61 35 100 100 100 100 4691 4704 .558 1.791 1.74 1.795 1.766 1.221 80 349 1.86 .96 110 2250 9620 48 59 95 106 0 2702 73 2629 1.564 2682 2609 .639 1.519 .645 .603
6 412 191 347 90 65 101 361 96 354 97 14 6 0 0 213 275 107 78 21 21 11 15 166 20 .644 1.554 .429 .505 .535 3.938 120 366 1.568 .79 120 2370 9620 48 60 107 119 -100 167 79 88 1.357 84 5 .737 .374 .441 -1.418
7 1858 2132 350 91 1508 2041 1842 2108 355 95 1492 2017 0 0 297 335 66 34 100 100 100 100 3549 3509 .739 1.353 1.352 1.362 1.325 1.235 80 288 1.418 .95 110 2520 9620 48 59 122 133 0 1862 79 1783 1.182 1841 1762 .846 1.181 .241 .24
8 2065 2466 358 90 1707 2376 2090 2549 358 94 1732 2459 0 0 306 453 69 35 100 100 100 100 4083 4191 .718 1.392 1.42 1.387 1.437 1.233 80 293 1.462 .95 100 2660 9620 49 59 137 147 0 2154 79 2075 1.216 2226 2148 .823 1.24 .282 .31
9 1407 1477 367 93 1040 1384 1398 1478 365 98 1031 1385 0 0 351 396 69 42 100 100 100 100 2424 2416 .751 1.331 1.343 1.358 1.306 1.346 32 97 1.348 .9 60 2790 9630 52 58 152 158 0 1290 81 1209 1.162 1291 1210 .86 1.173 .217 .231
10 423 127 356 91 67 36 420 119 355 97 64 28 0 0 90 47 69 42 49 33 20 12 103 92 1.861 .537 .438 .428 .39 3.878 120 411 1.375 .41 120 2910 9620 48 60 161 173 0 111 79 31 .469 104 24 2.131 .382 -1.091 -1.388
11 1719 225 361 92 1358 133 1755 215 364 96 1394 123 0 0 263 68 79 35 100 96 100 83 1491 1517 10.211 .098 .088 .089 .093 1.764 80 270 .162 .75 100 3060 9620 49 59 177 187 0 197 80 116 .086 188 107 11.691 .077 -3.547 -3.698
12 689 637 395 108 294 529 649 626 422 113 254 518 0 0 151 244 130 40 88 100 47 100 823 772 .556 1.799 2.039 1.822 1.707 1.858 80 263 2.233 .71 100 3190 9620 49 59 190 200 0 556 94 462 1.571 547 452 .636 1.781 .652 .833
13 669 514 370 112 299 402 660 502 387 121 290 390 0 0 117 109 105 46 96 100 80 100 701 680 .744 1.344 1.345 1.42 1.425 1.691 80 289 1.604 .77 110 3320 9620 48 59 202 213 0 449 98 351 1.174 438 341 .852 1.175 .232 .232
14 739 496 364 112 375 384 722 496 367 136 358 384 0 0 120 95 78 154 100 100 98 77 759 742 .977 1.024 1.073 1.044 1.071 1.53 80 304 1.396 .74 100 3460 9610 48 58 217 227 0 433 98 335 .894 433 335 1.118 .937 -.161 -.094
15 759 643 379 111 380 532 704 556 373 127 325 445 0 0 279 376 71 68 96 100 93 100 912 770 .714 1.4 1.369 1.512 1.447 1.756 32 125 1.455 .89 70 3600 9610 49 56 232 239 0 562 97 465 1.223 486 389 .818 1.196 .29 .258
16 681 343 375 107 306 236 417 132 375 114 42 25 0 0 669 519 73 48 35 35 20 22 542 67 1.297 .771 .595 .653 .658 2.687 120 366 .809 .95 120 3720 9620 48 60 242 254 -100 300 93 206 .674 115 22 1.485 .52 -.57 -.944
17 882 820 360 92 522 728 893 843 361 99 533 751 0 0 142 142 70 36 100 100 98 100 1250 1284 .717 1.395 1.409 1.431 1.369 1.47 80 292 1.485 .89 110 3860 9620 48 59 256 267 0 716 80 636 1.218 736 656 .821 1.231 .285 .299
18 526 300 376 96 150 204 515 296 385 116 139 200 0 0 100 70 85 69 76 96 46 86 354 339 .735 1.36 1.439 1.594 1.342 2.844 80 314 1.648 .62 100 4000 9610 48 58 271 281 0 262 84 178 1.188 259 175 .842 1.257 .248 .33
19 612 387 424 124 188 263 641 358 425 160 217 234 0 0 127 137 101 100 71 90 53 59 451 451 .715 1.399 1.078 1.386 1.444 2.071 32 148 1.976 .56 70 4120 9590 47 54 284 291 0 338 108 230 1.222 313 204 .818 .942 .289 -.087
20 1419 1529 398 102 1021 1427 1416 1476 405 119 1018 1374 0 0 226 272 84 65 100 100 100 100 2448 2392 .715 1.398 1.35 1.411 1.4 1.297 80 349 1.446 .93 110 4260 9610 47 58 296 307 0 1335 89 1246 1.221 1289 1200 .819 1.179 .288 .237

Total number of rows: 44544

Table truncated, full table size 9549 Kbytes.




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