NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88431 Query DataSets for GSM88431
Status Public on Dec 21, 2005
Title N-56, NORM, M, GSF, 6 x ETOH, 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 ETOH
Organism Homo sapiens
Characteristics nGSF56, 14 days DMEM F12 12.9% D/S FCS + 6 x ETOH
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15581.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
1 481 350 338 145 143 205 470 339 344 168 132 194 0 0 88 131 85 89 84 75 28 56 348 326 .698 1.434 1.47 1.203 1.167 2.742 32 153 2.978 .42 60 1950 9960 69 75 60 66 0 277 115 162 1.133 268 153 .882 1.162 .18 .216
2 741 491 372 143 369 348 723 517 371 154 351 374 0 0 249 272 78 63 87 81 75 71 717 725 1.06 .943 1.066 .888 .873 2.653 32 169 1.181 .83 70 2080 9980 70 77 72 79 0 388 113 275 .745 409 296 1.341 .842 -.424 -.248
3 1796 1429 363 135 1433 1294 1854 1427 363 146 1491 1292 0 0 447 398 75 64 100 100 100 100 2727 2783 1.107 .903 .867 .913 .901 1.422 80 305 .937 .94 100 2210 9970 68 78 84 94 0 1130 107 1023 .714 1128 1021 1.401 .685 -.486 -.546
4 543 344 342 138 201 206 451 296 340 153 109 158 0 0 220 183 77 69 68 84 40 53 407 267 .976 1.025 1.45 1.017 1.048 2.572 32 134 1.471 .61 70 2350 9980 70 77 99 106 0 272 109 163 .81 234 125 1.234 1.146 -.304 .196
5 1159 2628 330 148 829 2480 1200 2705 336 155 870 2557 0 0 238 609 74 61 100 100 98 100 3309 3427 .334 2.992 2.939 3.057 2.946 1.334 80 397 3.082 .94 110 2480 9970 67 78 110 121 0 2077 117 1960 2.365 2138 2021 .423 2.323 1.242 1.216
6 453 303 328 147 125 156 440 285 335 153 112 138 0 0 162 132 73 58 53 75 43 53 281 250 .801 1.248 1.232 .954 .939 2.626 32 167 1.642 .56 70 2620 9980 70 77 126 133 0 240 116 123 .986 225 109 1.014 .974 -.02 -.038
7 1031 1240 335 143 696 1097 1070 1209 341 148 735 1066 0 0 259 307 74 58 98 100 98 100 1793 1801 .634 1.576 1.45 1.61 1.564 1.519 80 340 1.666 .9 110 2750 9970 67 78 137 148 0 980 113 867 1.246 956 843 .803 1.146 .317 .197
8 1218 876 348 149 870 727 1200 881 356 158 852 732 0 0 248 243 77 73 100 100 100 98 1597 1584 1.197 .836 .859 .806 .846 1.545 80 304 .966 .89 100 2880 9970 68 78 151 161 0 692 118 575 .661 696 579 1.514 .679 -.598 -.558
9 1164 683 365 158 799 525 1196 641 372 174 831 483 0 0 357 243 85 94 100 100 100 96 1324 1314 1.522 .657 .581 .661 .696 1.514 32 143 .814 .83 70 3030 9980 70 77 167 174 0 540 125 415 .519 507 382 1.925 .459 -.945 -1.122
10 444 210 388 144 56 66 442 196 396 155 54 52 0 0 98 88 89 74 30 43 10 18 122 106 .848 1.179 .963 .787 .796 3.666 120 384 12.051 .07 120 3150 9970 67 79 177 189 0 166 114 52 .932 155 41 1.073 .761 -.102 -.394
11 1281 243 423 146 858 97 1287 229 432 154 864 83 0 0 276 84 93 62 98 60 98 28 955 947 8.845 .113 .096 .107 .107 2.525 80 234 .439 .44 100 3290 9970 68 78 192 202 0 192 115 77 .089 181 66 11.19 .076 -3.484 -3.719
12 665 484 430 155 235 329 644 489 434 163 214 334 0 0 132 140 98 75 86 96 59 92 564 548 .714 1.4 1.561 1.42 1.413 2.291 52 251 2.604 .52 90 3420 9970 68 77 205 214 0 383 123 260 1.107 387 264 .904 1.234 .146 .303
13 657 370 451 176 206 194 643 364 459 197 192 188 0 0 115 96 101 123 81 71 46 28 400 380 1.062 .942 .979 .935 .959 2.053 32 154 2.629 .39 70 3560 9970 69 76 220 227 0 292 139 153 .744 288 149 1.343 .774 -.426 -.37
14 520 302 430 173 90 129 504 300 435 193 74 127 0 0 120 119 93 101 45 60 22 23 219 201 .698 1.433 1.716 1.071 1.077 3.467 120 453 3.391 .3 120 3690 9970 67 79 231 243 0 239 137 102 1.133 237 100 .883 1.357 .18 .44
15 611 430 411 189 200 241 620 453 412 197 209 264 0 0 115 119 79 82 84 87 59 68 441 473 .83 1.205 1.263 1.299 1.347 2.196 32 167 2.68 .41 70 3840 9970 69 76 248 255 0 340 149 190 .952 358 209 1.05 .998 -.07 -.002
16 929 523 400 168 529 355 930 514 401 178 530 346 0 0 184 163 83 83 98 95 96 90 884 876 1.49 .671 .653 .638 .661 1.711 80 310 .906 .8 100 3970 9960 67 77 260 270 0 413 133 281 .53 406 273 1.885 .516 -.915 -.954
17 673 453 434 150 239 303 654 432 429 160 220 282 0 0 136 153 91 67 86 94 67 88 542 502 .789 1.268 1.282 1.343 1.206 2.859 52 254 2.24 .52 90 4110 9970 68 77 274 283 0 358 119 240 1.002 341 223 .998 1.013 .003 .019
18 539 411 446 142 93 269 526 395 447 153 80 253 0 0 94 124 97 64 46 98 13 90 362 333 .346 2.892 3.163 2.653 2.283 2.681 52 183 4.546 .32 80 4240 9980 70 78 288 296 0 325 112 213 2.286 312 200 .437 2.5 1.193 1.322
19 493 283 456 149 37 134 488 268 459 158 32 119 0 0 100 128 91 64 28 65 11 46 171 151 .276 3.622 3.719 1.678 1.55 2.961 120 407 8.088 .14 120 4370 9970 67 79 299 311 0 224 118 106 2.863 212 94 .349 2.939 1.517 1.556
20 1202 1024 467 139 735 885 1169 985 473 150 702 846 0 0 194 185 94 59 100 100 100 100 1620 1548 .831 1.204 1.205 1.225 1.146 1.414 52 194 1.278 .87 90 4510 9970 68 77 314 323 0 809 110 700 .952 779 669 1.051 .953 -.071 -.07

Total number of rows: 44544

Table truncated, full table size 9634 Kbytes.




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