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Sample GSM88440 Query DataSets for GSM88440
Status Public on Dec 21, 2005
Title N-56, NORM, M, GSF, 1 x ETOH, 24h
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 nGSF56, proliferating, 24h ETOH
Organism Homo sapiens
Characteristics nGSF56, proliferating, 24h ETOH
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16657.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
1 840 1361 451 235 389 1126 829 848 465 249 378 613 0 0 226 1363 127 118 88 98 73 84 1515 991 .345 2.895 1.622 2.109 1.612 2.743 52 282 5.339 .62 80 1700 9400 52 60 66 74 -100 1226 212 1014 2.607 764 552 .384 1.46 1.382 .546
2 1191 1912 458 212 733 1700 1165 1498 452 231 707 1286 0 0 517 1549 91 158 84 96 84 90 2433 1993 .431 2.319 1.819 1.911 1.52 2.101 32 128 3.549 .72 60 1840 9420 55 61 81 87 -100 1722 191 1531 2.089 1349 1158 .479 1.638 1.063 .712
3 3116 2873 474 205 2642 2668 3108 2673 468 216 2634 2468 0 0 863 963 98 126 100 100 100 100 5310 5102 .99 1.01 .937 1.017 .934 1.454 80 248 1.184 .92 100 1970 9400 51 61 92 102 0 2587 185 2403 .909 2407 2223 1.1 .844 -.137 -.245
4 605 548 479 200 126 348 478 234 477 203 -1 34 0 0 370 770 100 70 23 35 17 27 474 33 .362 2.762 null 1.049 .952 4.533 120 362 3.669 .73 120 2080 9400 50 62 102 114 -100 493 180 313 2.487 211 31 .402 null 1.315 null
5 2712 3711 466 194 2246 3517 2310 3196 470 199 1844 3002 0 0 2213 2385 101 60 100 100 100 100 5763 4846 .639 1.566 1.628 1.623 1.596 1.333 80 291 1.398 .93 110 2230 9400 50 61 117 128 0 3342 175 3167 1.41 2878 2703 .709 1.466 .496 .552
6 541 514 471 183 70 331 437 233 484 190 -34 50 0 0 274 763 153 67 20 45 15 33 401 16 .211 4.729 null .88 1.066 5.297 120 386 4.18 .63 120 2350 9400 50 62 129 141 -100 463 165 298 4.258 210 45 .235 null 2.09 null
7 2117 2033 459 178 1658 1855 2052 1775 461 188 1593 1597 0 0 462 914 91 65 100 100 100 100 3513 3190 .894 1.119 1.003 1.062 .983 1.508 80 322 1.437 .84 110 2510 9400 50 61 145 156 0 1831 160 1670 1.008 1598 1438 .993 .903 .011 -.148
8 2761 2427 449 177 2312 2250 2826 2284 460 190 2377 2107 0 0 447 754 92 63 100 100 100 100 4562 4484 1.028 .973 .886 .944 .913 1.318 80 278 1.124 .92 100 2640 9400 51 61 159 169 0 2186 159 2026 .876 2057 1897 1.141 .798 -.19 -.325
9 1725 1992 462 179 1263 1813 1860 1836 467 185 1398 1657 0 0 791 1091 97 55 90 100 88 100 3076 3055 .697 1.435 1.185 1.561 1.384 2.186 52 193 1.712 .82 80 2790 9400 52 60 175 183 0 1794 161 1633 1.293 1653 1492 .774 1.067 .37 .094
10 831 826 436 174 395 652 806 396 443 177 370 222 0 0 228 855 100 57 94 92 76 80 1047 592 .606 1.651 .6 .936 .717 2.627 52 177 3.7 .66 80 2910 9390 51 59 187 195 -100 744 157 587 1.486 357 200 .673 .54 .572 -.888
11 2411 703 446 168 1965 535 2579 389 456 178 2133 221 0 0 702 613 112 81 100 86 98 65 2500 2354 3.673 .272 .104 .156 .145 2.941 80 301 .69 .62 100 3040 9400 51 61 199 209 0 633 151 482 .245 350 199 4.079 .093 -2.028 -3.422
12 997 942 445 168 552 774 945 626 458 174 500 458 0 0 251 909 101 76 100 97 95 95 1326 958 .713 1.402 .916 1.089 .995 1.973 80 266 3.316 .63 100 3170 9400 51 61 212 222 -100 848 151 697 1.263 564 412 .792 .825 .337 -.278
13 1079 1006 455 170 624 836 1089 728 464 178 634 558 0 0 225 729 98 70 100 96 97 92 1460 1192 .746 1.34 .88 1.029 .985 2.063 80 238 2.447 .71 100 3310 9400 51 61 226 236 -100 906 153 753 1.206 656 502 .829 .793 .271 -.335
14 978 864 478 161 500 703 951 608 483 178 473 447 0 0 257 809 100 68 96 100 90 98 1203 920 .711 1.406 .945 1.204 1.124 1.865 80 285 2.937 .67 100 3440 9390 50 60 239 249 -100 778 145 633 1.266 548 403 .79 .851 .34 -.233
15 1260 1120 483 150 777 970 1259 991 490 162 776 841 0 0 257 523 96 55 100 100 100 100 1747 1617 .801 1.248 1.084 1.14 1.093 1.629 52 238 1.589 .84 90 3580 9400 51 60 253 262 0 1009 135 874 1.124 892 757 .89 .976 .169 -.035
16 2262 1861 496 139 1766 1722 2226 1805 520 151 1730 1666 0 0 333 479 149 67 100 100 100 100 3488 3396 1.026 .975 .963 .958 .918 1.356 52 260 1.021 .9 90 3700 9380 49 58 265 274 0 1676 125 1551 .878 1625 1500 1.139 .867 -.188 -.206
17 1414 1339 535 137 879 1202 1447 1201 559 150 912 1064 0 0 267 403 156 67 100 100 96 100 2081 1976 .731 1.367 1.167 1.388 1.334 1.464 52 278 1.56 .86 90 3840 9390 50 59 279 288 0 1206 123 1082 1.231 1082 958 .812 1.051 .3 .071
18 1026 476 551 136 475 340 1019 473 559 146 468 337 0 0 183 95 115 51 98 100 90 100 815 805 1.397 .716 .72 .747 .754 1.701 52 277 .897 .75 90 3990 9390 50 59 294 303 0 429 122 306 .645 426 303 1.551 .648 -.634 -.625
19 915 514 568 138 347 376 912 466 575 146 344 328 0 0 140 220 116 52 96 98 80 96 723 672 .923 1.084 .953 1.004 1.049 1.93 52 225 1.504 .68 90 4130 9400 51 60 308 317 0 463 124 339 .976 420 295 1.025 .859 -.035 -.22
20 2076 1727 589 152 1487 1575 2105 1764 598 156 1516 1612 0 0 518 538 111 46 98 100 97 100 3062 3128 .944 1.059 1.063 1.07 1.027 1.476 80 248 1.113 .94 100 4260 9390 50 60 321 331 0 1555 137 1418 .954 1589 1452 1.048 .958 -.068 -.063

Total number of rows: 44544

Table truncated, full table size 9952 Kbytes.




Supplementary data files not provided
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