NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88426 Query DataSets for GSM88426
Status Public on Dec 21, 2005
Title N-58, NORM, M, GSF, 6 x 100nM DHT, 14d
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, G0, 6 x 100nM DHT, 14 days
Organism Homo sapiens
Characteristics nGSF58, 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/2001-06/17307.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
1 249 82 225 74 24 8 241 77 228 81 16 3 0 0 65 33 48 34 31 20 14 5 32 19 3 .333 .188 .466 .494 3.171 120 537 3.143 .17 120 1260 9390 45 57 44 56 -100 102 92 10 .413 95 4 2.419 .233 -1.274 -2.104
2 252 180 228 79 24 101 230 66 228 89 2 -13 0 0 87 252 47 38 25 24 15 22 125 -11 .238 4.208 null 1.428 1.291 3.289 120 350 4.677 .57 120 1400 9390 45 57 58 70 -100 223 98 125 5.219 82 -16 .192 null 2.384 null
3 1309 843 220 59 1089 784 1362 912 225 61 1142 853 0 0 243 284 50 20 100 97 100 96 1873 1995 1.389 .72 .747 .635 .73 1.881 80 225 .862 .9 100 1540 9390 46 56 73 83 0 1045 73 972 .893 1131 1058 1.12 .926 -.163 -.11
4 231 76 213 59 18 17 215 52 214 60 2 -7 0 0 74 67 48 18 26 22 10 17 35 -5 1.059 .944 null .626 .633 3.192 120 374 1.788 .42 120 1670 9390 45 57 85 97 -100 94 73 21 1.171 64 -9 .854 null .228 null
5 1055 1888 220 59 835 1829 1104 1940 223 62 884 1881 0 0 258 292 51 31 98 100 95 100 2664 2765 .457 2.19 2.128 2.432 2.146 1.867 80 372 2.276 .91 110 1810 9390 45 56 99 110 0 2342 73 2268 2.717 2406 2333 .368 2.639 1.442 1.4
6 378 256 224 55 154 201 342 266 227 56 118 211 0 0 159 188 50 15 71 78 53 68 355 329 .766 1.305 1.788 .983 1.084 3.364 32 132 1.681 .68 60 1940 9400 49 55 115 121 0 317 68 249 1.619 330 262 .618 2.218 .695 1.149
7 891 1063 228 61 663 1002 908 1082 232 63 680 1021 0 0 139 198 50 19 100 100 100 100 1665 1701 .662 1.511 1.501 1.516 1.435 1.333 80 314 1.632 .92 100 2080 9390 46 56 127 137 0 1318 76 1243 1.874 1342 1266 .534 1.862 .906 .897
8 1450 1774 236 70 1214 1704 1493 1860 236 69 1257 1790 0 0 281 414 48 20 100 100 100 100 2918 3047 .712 1.404 1.424 1.391 1.385 1.341 80 310 1.509 .94 100 2220 9380 45 55 141 151 0 2200 87 2113 1.741 2307 2220 .574 1.766 .8 .821
9 761 478 227 60 534 418 783 433 230 61 556 373 0 0 252 138 44 19 100 100 96 100 952 929 1.278 .783 .671 .856 .8 1.612 32 135 .767 .86 70 2360 9400 48 55 156 163 0 593 74 518 .971 537 463 1.03 .832 -.043 -.265
10 247 71 230 69 17 2 248 71 234 71 18 2 0 0 47 24 46 24 30 17 5 4 19 20 8.5 .118 .111 .521 .446 4.116 120 404 3.758 .12 120 2480 9390 45 57 166 178 0 88 86 2 .146 88 2 6.854 .138 -2.777 -2.859
11 1031 112 234 73 797 39 1041 109 236 75 807 36 0 0 193 31 48 24 100 63 100 31 836 843 20.436 .049 .045 .053 .053 1.987 80 311 .172 .5 110 2620 9390 45 56 180 191 0 139 91 48 .061 135 45 16.478 .055 -4.042 -4.176
12 315 255 228 73 87 182 303 239 230 79 75 166 0 0 68 92 48 40 71 98 32 96 269 241 .478 2.092 2.213 2.379 2.128 2.31 52 201 2.704 .55 80 2760 9380 46 54 196 204 0 316 91 226 2.594 296 206 .385 2.745 1.375 1.457
13 391 231 227 77 164 154 398 239 234 97 171 162 0 0 69 53 86 164 87 47 48 0 318 333 1.065 .939 .947 .994 .926 1.973 80 268 1.268 .68 100 2890 9390 46 56 208 218 0 286 95 191 1.165 296 201 .859 1.175 .22 .233
14 409 220 231 80 178 140 410 224 229 84 179 144 0 0 84 59 46 28 93 96 87 93 318 323 1.271 .787 .804 .83 .832 2.197 80 250 1.201 .63 100 3020 9380 45 55 221 231 0 273 99 174 .975 278 179 1.025 .998 -.036 -.003
15 232 88 226 74 6 14 226 80 224 76 0 6 0 0 55 41 49 26 19 24 5 13 20 6 .429 2.333 null .567 .454 4.164 120 314 4.194 .15 120 3160 9390 45 57 234 246 0 109 92 17 2.894 99 7 .346 null 1.533 null
16 253 128 223 72 30 56 247 101 222 73 24 29 0 0 65 81 55 24 27 55 9 38 86 53 .536 1.867 1.208 1.05 1.021 4.668 120 334 2.956 .32 120 3290 9390 45 57 247 259 0 159 89 69 2.315 125 36 .432 1.499 1.211 .584
17 274 137 228 72 46 65 268 97 232 72 40 25 0 0 71 103 53 21 40 54 14 35 111 65 .708 1.413 .625 .814 .884 3.563 120 332 2.481 .48 120 3430 9390 45 57 261 273 0 170 89 81 1.752 120 31 .571 .775 .809 -.367
18 402 244 247 65 155 179 392 247 246 66 145 182 0 0 77 66 47 19 91 98 81 96 334 327 .866 1.155 1.255 1.214 1.1 2.105 80 245 1.403 .71 100 3570 9380 45 55 276 286 0 303 81 222 1.432 306 226 .698 1.557 .518 .638
19 402 247 252 66 150 181 399 245 251 68 147 179 0 0 83 54 50 21 92 98 71 98 331 326 .829 1.207 1.218 1.252 1.179 1.926 80 301 1.459 .66 110 3700 9380 44 55 288 299 0 306 82 224 1.497 304 222 .668 1.51 .582 .595
20 1101 954 254 66 847 888 1086 897 257 68 832 831 0 0 268 398 49 21 100 100 100 100 1735 1663 .954 1.048 .999 1.019 .995 1.352 80 246 1.277 .88 100 3840 9380 45 55 303 313 0 1183 82 1101 1.3 1112 1031 .769 1.239 .379 .309

Total number of rows: 44544

Table truncated, full table size 9325 Kbytes.




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