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Sample GSM88462 Query DataSets for GSM88462
Status Public on Dec 21, 2005
Title N-52, NORM, M, GSF
Sample type RNA
 
Channel 1
Source name mixed reference (CRG + FR)
Organism Homo sapiens
Characteristics mixed reference (CRG + FR)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name nGSF52, 14 days DMEM F12, 12.9% FCS, Go, against mixed reference (CRG + FR)
Organism Homo sapiens
Characteristics nGSF52, 14 days DMEM F12, 12.9% FCS, Go, against mixed reference (CRG + FR)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16278.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 1002 1367 359 213 643 1154 1000 1217 553 533 641 1004 0 0 189 663 508 1057 81 46 3 6 1797 1645 .557 1.795 1.566 1.69 1.558 1.648 32 120 3.621 .79 60 1540 9340 79 85 47 53 0 1163 181 982 1.527 1036 854 .655 1.333 .611 .415
2 434 410 328 199 106 211 347 232 366 250 19 33 0 0 235 444 234 425 15 17 10 9 317 52 .502 1.991 1.737 1.858 1.694 3.795 120 474 2.686 .68 120 1710 9310 73 85 61 73 -100 349 169 180 1.694 197 28 .59 1.478 .761 .564
3 2714 2542 338 206 2376 2336 2712 2419 346 219 2374 2213 0 0 656 975 84 77 100 100 100 100 4712 4587 1.017 .983 .932 .927 .991 1.527 52 233 1.142 .91 90 1810 9310 74 83 72 81 0 2163 175 1988 .837 2059 1883 1.195 .793 -.257 -.334
4 1216 1182 331 185 885 997 1195 1215 334 208 864 1030 0 0 340 400 85 76 100 100 100 100 1882 1894 .888 1.127 1.192 1.119 1.058 1.625 12 104 1.34 .83 50 1950 9320 77 82 88 93 -100 1006 157 849 .959 1034 877 1.043 1.015 -.061 .021
5 1853 4177 318 191 1535 3986 1826 3686 332 219 1508 3495 0 0 713 1810 95 134 100 100 100 100 5521 5003 .385 2.597 2.318 2.665 2.798 1.609 80 338 2.934 .87 100 2090 9320 75 85 100 110 0 3555 163 3392 2.21 3137 2975 .452 1.973 1.144 .98
6 395 339 331 202 64 137 335 214 363 273 4 12 0 0 223 364 143 225 13 15 10 9 201 16 .467 2.141 3 1.095 1.237 4.088 120 377 2.347 .67 120 2250 9310 73 85 115 127 -100 289 172 117 1.822 182 10 .549 2.553 .865 1.352
7 1478 1917 313 186 1165 1731 1492 1888 316 190 1179 1702 0 0 552 745 62 50 98 100 97 100 2896 2881 .673 1.486 1.444 1.596 1.482 1.788 80 210 1.577 .92 100 2360 9320 75 85 127 137 0 1632 158 1473 1.265 1607 1449 .791 1.229 .339 .297
8 1450 1826 313 188 1137 1638 1470 1813 322 195 1157 1625 0 0 498 644 71 56 100 100 100 100 2775 2782 .694 1.441 1.404 1.493 1.49 1.485 80 295 1.535 .91 100 2500 9320 75 85 141 151 0 1554 160 1394 1.226 1543 1383 .816 1.195 .294 .257
9 467 335 324 194 143 141 376 238 334 211 52 44 0 0 273 256 81 80 37 37 21 21 284 96 1.014 .986 .846 1.007 1.194 3.758 32 135 1.963 .5 60 2640 9290 74 80 157 163 -100 285 165 120 .839 203 37 1.192 .72 -.253 -.474
10 811 839 339 207 472 632 814 716 350 214 475 509 0 0 199 522 80 60 100 96 94 92 1104 984 .747 1.339 1.072 1 1.053 2.42 52 201 2.038 .78 80 2780 9310 75 83 170 178 0 714 176 538 1.14 609 433 .878 .912 .189 -.133
11 1783 587 342 210 1441 377 1875 502 350 228 1533 292 0 0 489 294 86 94 100 84 100 73 1818 1825 3.822 .262 .19 .227 .254 1.985 52 215 .461 .76 90 2900 9310 74 83 181 190 0 500 179 321 .223 427 249 4.491 .162 -2.167 -2.625
12 1131 1253 354 221 777 1032 1158 1318 361 228 804 1097 0 0 370 411 83 71 98 100 98 98 1809 1901 .753 1.328 1.364 1.307 1.285 1.611 52 240 1.437 .88 80 3040 9310 75 83 196 204 0 1066 188 878 1.13 1122 934 .885 1.161 .177 .216
13 1010 1134 355 233 655 901 921 874 366 241 566 641 0 0 334 770 86 71 98 92 98 90 1556 1207 .727 1.376 1.133 1.08 1.202 2.022 52 267 1.89 .87 80 3190 9310 75 83 211 219 -100 965 198 767 1.171 744 546 .854 .964 .227 -.053
14 1276 2039 351 242 925 1797 1298 1617 363 258 947 1375 0 0 345 1105 89 78 100 100 100 100 2722 2322 .515 1.943 1.452 1.733 1.628 1.614 32 188 2.47 .84 70 3340 9300 74 81 226 233 -100 1735 206 1529 1.653 1376 1170 .605 1.236 .725 .305
15 2089 6036 349 276 1740 5760 2125 5814 357 305 1776 5538 0 0 415 1954 98 224 100 100 100 100 7500 7314 .302 3.31 3.118 3.107 3.393 1.606 32 170 4.214 .85 70 3450 9320 76 83 237 244 0 5137 235 4902 2.817 4948 4713 .355 2.654 1.494 1.408
16 1133 786 330 240 803 546 1159 806 339 259 829 566 0 0 415 341 89 162 93 85 86 75 1349 1395 1.471 .68 .683 .685 .677 1.82 120 392 .947 .83 120 3600 9310 73 85 250 262 0 669 204 465 .579 686 482 1.728 .581 -.789 -.783
17 918 1154 309 214 609 940 831 834 318 219 522 620 0 0 406 818 68 58 98 100 93 98 1549 1142 .648 1.544 1.188 1.428 1.538 1.723 80 239 1.963 .89 100 3740 9310 74 84 265 275 -100 982 182 800 1.314 710 528 .761 1.011 .394 .016
18 594 1245 313 206 281 1039 582 1206 320 212 269 1000 0 0 136 317 70 58 92 100 83 100 1320 1269 .27 3.698 3.717 4.143 3.762 1.979 80 264 4.165 .76 100 3880 9310 74 84 279 289 0 1060 175 884 3.147 1026 851 .318 3.164 1.654 1.662
19 675 490 334 222 341 268 642 483 341 227 308 261 0 0 166 172 80 55 96 84 88 78 609 569 1.272 .786 .847 .73 .804 2.146 52 177 1.21 .71 80 4010 9310 75 83 293 301 0 417 189 228 .669 411 222 1.495 .721 -.58 -.472
20 1081 965 341 231 740 734 999 862 351 235 658 631 0 0 384 399 75 57 100 97 96 96 1474 1289 1.008 .992 .959 .967 .962 1.64 80 256 1.152 .88 100 4140 9310 74 84 305 315 0 821 197 625 .844 734 537 1.185 .816 -.244 -.293

Total number of rows: 43392

Table truncated, full table size 9313 Kbytes.




Supplementary data files not provided
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