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Sample GSM88459 Query DataSets for GSM88459
Status Public on Dec 21, 2005
Title ARD465, CAIS, F, GSF, mosaicism
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 ARD465,14 days of DMEM F12, 12.9% FCS, Go
Organism Homo sapiens
Characteristics ARD465,14 days of DMEM F12, 12.9% FCS, Go
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16471.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
1 647 468 222 184 425 284 635 432 224 190 413 248 0 0 163 208 53 46 100 94 100 88 709 661 1.496 .668 .6 .601 .677 1.849 52 335 .963 .79 90 1690 9140 57 66 48 57 0 651 256 395 .929 601 345 1.076 .835 -.106 -.26
2 1218 1699 229 199 989 1500 556 855 226 201 327 656 0 0 2003 2356 55 41 78 96 65 90 2489 983 .659 1.517 2.006 1.672 1.692 4.626 32 119 2.076 .59 60 1830 9170 62 68 64 70 -100 2362 277 2085 2.109 1189 912 .474 2.789 1.076 1.48
3 2227 1218 240 210 1987 1008 1825 1050 242 209 1585 840 0 0 1135 720 56 46 100 96 98 93 2995 2425 1.971 .507 .53 .453 .482 1.954 80 282 .648 .86 100 1960 9150 58 68 75 85 0 1693 292 1401 .705 1460 1168 1.418 .737 -.504 -.441
4 291 316 240 223 51 93 274 249 246 222 34 26 0 0 93 336 55 45 35 31 17 10 144 60 .548 1.824 .765 1.007 1.119 3.353 120 370 6.299 .44 120 2120 9140 56 68 90 102 -100 439 310 129 2.535 346 36 .394 1.063 1.342 .088
5 1552 1528 242 224 1310 1304 1588 1548 248 225 1346 1324 0 0 403 478 53 45 100 100 100 98 2614 2670 1.005 .995 .984 .936 1.039 1.818 80 211 1.171 .88 100 2240 9150 58 68 103 113 0 2124 311 1813 1.384 2152 1841 .723 1.368 .469 .452
6 267 267 256 235 11 32 239 245 258 241 -17 10 0 0 104 134 58 73 19 14 10 8 43 -7 .344 2.909 null 1.169 1.111 3.773 120 351 3.783 .36 120 2390 9140 56 68 117 129 -100 371 327 44 4.045 341 14 .247 null 2.016 null
7 1419 1214 262 240 1157 974 1421 1190 264 248 1159 950 0 0 445 339 63 87 100 100 100 100 2131 2109 1.188 .842 .82 .86 .801 1.586 80 217 .947 .88 100 2510 9150 58 68 130 140 0 1688 334 1354 1.17 1654 1321 .854 1.14 .227 .189
8 1956 2947 270 242 1686 2705 1817 2725 273 250 1547 2483 0 0 772 1134 67 64 100 100 98 100 4391 4030 .623 1.604 1.605 1.702 1.581 1.755 80 330 1.728 .9 110 2650 9150 57 68 143 154 0 4097 336 3761 2.231 3789 3452 .448 2.232 1.157 1.158
9 2060 1340 285 250 1775 1090 1898 1351 294 264 1613 1101 0 0 574 380 74 87 100 100 100 100 2865 2714 1.628 .614 .683 .611 .633 1.359 32 131 .724 .88 60 2800 9140 59 65 161 167 0 1863 348 1515 .854 1878 1531 1.171 .949 -.228 -.076
10 342 278 264 249 78 29 327 256 268 256 63 7 0 0 118 115 63 66 49 25 27 15 107 70 2.69 .372 .111 .83 .733 4.096 120 366 1.917 .46 120 2940 9140 56 68 172 184 0 387 346 40 .517 356 10 1.935 .154 -.952 -2.695
11 1596 349 251 259 1345 90 1563 337 260 266 1312 78 0 0 465 108 58 60 100 56 100 33 1435 1390 14.944 .067 .059 .076 .085 2.157 80 249 .227 .55 100 3060 9140 57 67 185 195 0 485 360 125 .093 469 108 10.749 .083 -3.426 -3.597
12 659 605 265 260 394 345 652 536 310 382 387 276 0 0 168 217 269 486 78 25 18 0 739 663 1.142 .876 .713 .814 .856 1.825 32 179 1.184 .82 70 3200 9130 57 64 200 207 0 841 361 480 1.217 745 384 .821 .992 .284 -.012
13 742 607 274 257 468 350 724 561 336 344 450 304 0 0 189 193 307 406 75 36 21 1 818 754 1.337 .748 .676 .697 .639 1.748 52 255 1.233 .73 90 3340 9140 57 66 213 222 0 844 357 487 1.04 780 423 .962 .939 .056 -.09
14 627 423 278 281 349 142 637 413 282 278 359 132 0 0 120 102 65 54 100 77 97 58 491 491 2.458 .407 .368 .361 .385 2.39 80 300 .912 .62 100 3480 9140 57 67 227 237 0 588 391 197 .566 574 184 1.768 .511 -.822 -.968
15 1005 1019 287 280 718 739 989 961 297 270 702 681 0 0 348 438 74 63 100 100 100 93 1457 1383 .972 1.029 .97 .947 .904 1.65 32 158 1.26 .84 70 3620 9150 59 66 242 249 0 1417 389 1027 1.431 1336 947 .699 1.349 .517 .432
16 1593 1009 273 284 1320 725 1641 1002 279 282 1368 718 0 0 344 182 66 58 100 100 100 100 2045 2086 1.821 .549 .525 .556 .537 1.348 80 292 .603 .91 100 3750 9140 57 67 254 264 0 1403 395 1008 .764 1393 998 1.31 .73 -.389 -.455
17 733 579 274 294 459 285 725 585 280 290 451 291 0 0 173 97 64 52 97 98 97 96 744 742 1.611 .621 .645 .637 .603 1.74 80 246 .802 .81 100 3890 9140 57 67 268 278 0 805 409 396 .863 813 405 1.158 .897 -.212 -.157
18 522 430 279 294 243 136 529 426 286 299 250 132 0 0 132 110 68 56 91 72 81 55 379 382 1.787 .56 .528 .556 .588 2.142 80 246 .999 .71 100 4030 9140 57 67 282 292 0 598 409 189 .778 592 184 1.285 .734 -.362 -.446
19 540 702 280 291 260 411 560 680 286 294 280 389 0 0 160 165 69 47 86 100 76 98 671 669 .633 1.581 1.389 1.727 1.555 1.938 80 234 1.721 .77 100 4170 9150 58 68 296 306 0 976 405 571 2.198 945 541 .455 1.932 1.136 .95
20 1505 1281 276 298 1229 983 1391 1207 281 298 1115 909 0 0 542 450 65 51 100 100 98 98 2212 2024 1.25 .8 .815 .791 .798 1.65 80 234 .916 .88 100 4300 9140 57 67 309 319 0 1781 414 1367 1.112 1678 1264 .899 1.133 .153 .181

Total number of rows: 43392

Table truncated, full table size 9411 Kbytes.




Supplementary data files not provided
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