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Sample GSM88448 Query DataSets for GSM88448
Status Public on Dec 21, 2005
Title ARD842, CAIS, F, GOF
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 ARD842, CAIS 14 days DMEM F12, 12.9% FCS, Go, against mixed reference
Organism Homo sapiens
Characteristics ARD842, CAIS 14 days DMEM F12, 12.9% FCS, Go, against mixed reference
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16237.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 1862 2866 73 59 1789 2807 1351 1777 153 103 1278 1718 0 0 1223 2358 133 105 100 100 100 98 4596 2996 .637 1.569 1.344 1.382 1.599 1.945 80 457 2.146 .81 110 1730 9490 67 78 47 58 0 2871 59 2812 1.572 1780 1721 .636 1.347 .652 .429
2 199 300 66 56 133 244 65 64 131 108 -1 8 0 0 305 572 133 148 26 22 15 16 377 7 .545 1.835 null 1.103 1.2 4.544 120 412 2.334 .77 120 1880 9480 66 78 62 74 -100 300 56 244 1.838 64 8 .544 null .878 null
3 5405 6550 244 150 5161 6400 5363 6066 225 158 5119 5916 0 0 1824 3240 109 89 100 100 100 100 11561 11035 .806 1.24 1.156 1.129 1.209 1.616 52 207 1.472 .89 90 2000 9480 67 76 75 84 0 6561 150 6411 1.242 6076 5926 .805 1.158 .313 .211
4 368 356 281 170 87 186 289 187 284 180 8 17 0 0 297 534 67 63 25 32 14 19 273 25 .468 2.138 2.125 1.405 1.281 3.399 120 391 2.347 .75 120 2150 9480 66 78 89 101 -100 357 170 186 2.141 187 17 .467 2.129 1.099 1.09
5 3016 9949 274 164 2742 9785 2574 9801 280 172 2300 9637 0 0 1340 4218 63 51 100 100 100 100 12527 11937 .28 3.569 4.19 3.45 4.03 2.124 80 219 4.128 .84 100 2270 9490 68 78 102 112 0 9965 164 9801 3.574 9817 9653 .28 4.197 1.838 2.069
6 452 557 294 167 158 390 313 185 293 173 19 18 0 0 425 932 68 57 30 37 17 26 548 37 .405 2.468 .947 1.279 1.201 4.001 120 361 3.135 .69 120 2420 9480 66 78 116 128 -100 558 167 391 2.472 185 18 .404 .949 1.306 -.076
7 2480 2527 301 172 2179 2355 2006 1770 302 182 1705 1598 0 0 1582 2158 67 74 98 97 98 97 4534 3303 .925 1.081 .937 .885 .958 1.89 80 255 1.342 .91 110 2540 9490 67 78 128 139 0 2531 172 2359 1.083 1773 1601 .924 .939 .114 -.091
8 3159 5425 308 200 2851 5225 2925 4810 313 213 2617 4610 0 0 1651 3312 72 88 100 100 100 100 8076 7227 .546 1.833 1.762 1.724 1.871 1.743 80 294 2.024 .93 100 2670 9490 68 78 142 152 0 5434 200 5234 1.836 4818 4618 .545 1.764 .876 .819
9 461 612 322 222 139 390 388 320 329 229 66 98 0 0 236 531 70 84 48 51 28 48 529 164 .356 2.806 1.485 2.398 2.376 3.542 52 268 4.288 .52 90 2830 9480 67 76 158 167 -100 613 222 391 2.81 321 98 .356 1.487 1.491 .573
10 1265 1835 333 233 932 1602 974 995 344 244 641 762 0 0 1026 2079 74 82 77 69 70 65 2534 1403 .582 1.719 1.189 1.143 1.487 2.57 120 400 2.103 .91 120 2970 9480 66 78 171 183 -100 1838 233 1605 1.722 997 763 .581 1.191 .784 .252
11 2630 2075 332 249 2298 1826 2636 1452 341 256 2304 1203 0 0 1116 1802 74 86 100 92 100 90 4124 3507 1.258 .795 .522 .518 .567 2.255 52 227 1.259 .82 90 3080 9480 67 76 183 192 0 2078 249 1829 .796 1454 1205 1.256 .523 -.329 -.935
12 1318 1826 338 232 980 1594 1374 1705 345 253 1036 1473 0 0 577 1106 73 99 96 98 92 98 2574 2509 .615 1.627 1.422 1.522 1.755 1.995 52 223 1.87 .91 80 3230 9470 67 75 199 207 0 1829 232 1597 1.629 1708 1475 .614 1.424 .704 .51
13 1051 1005 334 223 717 782 1090 932 338 240 756 709 0 0 297 457 70 85 100 100 98 96 1499 1465 .917 1.091 .938 1.004 1.039 1.853 52 223 1.453 .81 80 3370 9480 68 76 213 221 0 1007 223 783 1.092 934 710 .915 .939 .128 -.09
14 1107 1161 341 223 766 938 1098 1212 341 234 757 989 0 0 319 552 70 79 100 96 100 90 1704 1746 .817 1.225 1.306 .998 1.14 2.36 52 213 1.653 .82 80 3510 9470 67 75 227 235 0 1163 223 940 1.227 1214 991 .815 1.309 .295 .388
15 1350 2257 339 219 1011 2038 1344 2316 342 225 1005 2097 0 0 496 841 71 76 100 100 98 100 3049 3102 .496 2.016 2.087 2.147 2.045 2.009 52 213 2.234 .86 80 3640 9480 68 76 240 248 0 2261 219 2041 2.019 2320 2100 .495 2.09 1.014 1.064
16 1821 1185 345 233 1476 952 1640 979 351 243 1295 746 0 0 584 601 71 82 100 100 100 100 2428 2041 1.55 .645 .576 .557 .595 1.53 80 377 .79 .91 110 3780 9480 66 77 252 263 0 1187 233 954 .646 981 747 1.548 .577 -.63 -.793
17 1223 1209 358 234 865 975 1251 1134 359 243 893 900 0 0 384 595 77 73 96 100 96 98 1840 1793 .887 1.127 1.008 1.026 1.14 1.963 52 266 1.434 .84 90 3930 9470 66 75 268 277 0 1211 234 977 1.129 1136 901 .886 1.01 .175 .014
18 882 752 370 245 512 507 842 550 372 256 472 305 0 0 266 553 80 82 97 81 93 67 1019 777 1.01 .99 .646 .692 .833 2.341 80 277 1.786 .77 100 4070 9470 66 76 282 292 0 753 245 508 .992 551 306 1.008 .647 -.012 -.628
19 1046 1932 375 270 671 1662 1003 1796 376 285 628 1526 0 0 349 874 78 100 100 100 100 100 2333 2154 .404 2.477 2.43 2.502 2.536 1.379 52 163 2.641 .91 80 4200 9480 68 76 296 304 0 1935 270 1665 2.481 1799 1529 .403 2.434 1.311 1.283
20 1701 1709 370 286 1331 1423 1591 1545 375 303 1221 1259 0 0 628 773 78 107 100 100 98 98 2754 2480 .935 1.069 1.031 1.028 1.094 1.655 80 308 1.234 .9 100 4330 9480 67 77 308 318 0 1712 286 1425 1.071 1548 1261 .934 1.033 .099 .047

Total number of rows: 43392

Table truncated, full table size 9319 Kbytes.




Supplementary data files not provided
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