NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM88454 Query DataSets for GSM88454
Status Public on Dec 21, 2005
Title N-57, 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 nGSF57, 14 days DMEM F12, 12.9% FCS, G0, against mixed reference
Organism Homo sapiens
Characteristics nGSF57, 14 days DMEM F12, 12.9% FCS, G0, against mixed reference
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16248.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
1 990 614 359 174 631 440 1008 613 360 181 649 439 0 0 170 112 83 60 100 100 100 100 1071 1088 1.434 .697 .676 .701 .683 1.422 52 321 .996 .76 90 1570 9290 48 57 40 49 0 526 149 377 .598 526 376 1.673 .58 -.742 -.786
2 749 994 360 165 389 829 703 936 358 171 343 771 0 0 301 530 76 54 81 87 75 84 1218 1114 .469 2.131 2.248 2.143 2.395 3.286 32 149 2.584 .73 60 1710 9280 49 55 56 62 0 852 141 711 1.827 803 661 .547 1.927 .87 .947
3 2557 1620 370 179 2187 1441 2651 1781 377 183 2281 1602 0 0 785 713 88 55 98 93 98 88 3628 3883 1.518 .659 .702 .564 .677 2.171 80 354 .79 .9 100 1850 9280 47 57 68 78 0 1389 153 1236 .565 1527 1374 1.77 .602 -.824 -.732
4 772 421 371 182 401 239 714 320 379 187 343 138 0 0 371 285 82 50 75 62 65 53 640 481 1.678 .596 .402 .708 .753 2.72 32 120 1.349 .55 60 1990 9300 51 57 84 90 0 361 156 205 .511 274 118 1.957 .345 -.968 -1.535
5 1991 2078 374 180 1617 1898 2102 2256 387 188 1728 2076 0 0 534 906 86 66 98 91 98 90 3515 3804 .852 1.174 1.201 .961 1.22 2.461 80 300 1.397 .92 100 2110 9280 47 57 94 104 0 1782 154 1627 1.006 1934 1780 .994 1.03 .009 .043
6 959 625 378 183 581 442 859 594 392 186 481 411 0 0 409 356 95 62 90 81 81 71 1023 892 1.314 .761 .854 .788 .983 2.09 32 100 1.019 .79 60 2250 9310 52 58 110 116 0 536 157 379 .652 509 352 1.533 .733 -.616 -.449
7 2417 2895 407 183 2010 2712 2375 2666 411 190 1968 2483 0 0 1109 1296 92 74 100 100 95 100 4722 4451 .741 1.349 1.262 1.503 1.382 1.729 80 314 1.368 .94 110 2380 9300 48 59 120 131 0 2482 157 2325 1.157 2286 2129 .864 1.082 .21 .113
8 2023 2570 414 187 1609 2383 2019 2416 428 240 1605 2229 0 0 740 1100 125 474 100 100 100 96 3992 3834 .675 1.481 1.389 1.513 1.491 1.439 80 335 1.59 .92 110 2520 9290 47 58 134 145 0 2204 160 2043 1.27 2072 1911 .787 1.191 .345 .252
9 789 857 406 207 383 650 567 714 424 345 161 507 0 0 527 625 127 748 56 34 37 12 1033 668 .589 1.697 3.149 1.643 1.517 4.036 32 133 2.328 .57 60 2660 9270 48 54 151 157 -100 735 177 557 1.455 612 435 .687 2.7 .541 1.433
10 1100 768 388 195 712 573 1090 709 400 225 702 514 0 0 348 411 91 159 100 80 98 67 1285 1216 1.243 .805 .732 .665 .808 2.582 52 258 1.112 .82 90 2790 9280 47 56 162 171 0 659 167 491 .69 608 441 1.449 .628 -.535 -.672
11 2189 729 402 197 1787 532 2422 546 406 206 2020 349 0 0 864 509 88 61 100 80 100 70 2319 2369 3.359 .298 .173 .214 .295 2.672 80 298 .499 .8 100 2930 9290 48 58 176 186 0 625 169 456 .255 468 299 3.917 .148 -1.97 -2.755
12 1366 1956 401 219 965 1737 1018 1618 403 225 617 1399 0 0 821 1177 91 73 92 100 77 100 2702 2016 .556 1.8 2.267 2.438 2.035 2.417 80 300 1.87 .86 100 3070 9290 48 58 190 200 0 1677 188 1489 1.543 1387 1200 .648 1.944 .626 .959
13 1275 1676 416 232 859 1444 1235 1553 420 240 819 1321 0 0 417 838 97 76 96 100 94 100 2303 2140 .595 1.681 1.613 1.6 1.5 2.016 52 232 2.133 .81 80 3220 9290 49 57 206 214 0 1437 199 1238 1.441 1332 1133 .694 1.383 .527 .468
14 1997 3688 418 241 1579 3447 2042 3440 423 242 1624 3199 0 0 547 1771 94 73 100 100 100 100 5026 4823 .458 2.183 1.97 1.942 2.407 1.936 52 204 2.759 .88 80 3360 9270 47 55 220 228 0 3162 207 2956 1.872 2950 2743 .534 1.689 .904 .756
15 2558 6327 405 228 2153 6099 2743 6230 406 234 2338 6002 0 0 996 2805 93 64 100 100 98 100 8252 8340 .353 2.833 2.567 2.858 2.81 2.353 52 198 3.111 .9 80 3480 9290 49 57 232 240 0 5425 195 5230 2.429 5342 5146 .412 2.201 1.28 1.138
16 1633 1238 394 217 1239 1021 1672 1247 397 225 1278 1030 0 0 320 314 88 61 100 100 100 100 2260 2308 1.214 .824 .806 .811 .807 1.483 80 325 .92 .9 110 3620 9290 47 58 244 255 0 1062 186 875 .707 1069 883 1.415 .691 -.501 -.533
17 1387 2011 398 216 989 1795 1218 1553 401 224 820 1337 0 0 695 1382 86 57 93 100 90 100 2784 2157 .551 1.815 1.63 1.701 1.82 1.952 80 306 2.148 .87 110 3760 9290 47 58 258 269 0 1724 185 1539 1.556 1332 1146 .643 1.398 .638 .483
18 906 929 407 215 499 714 901 867 413 222 494 652 0 0 210 369 86 63 100 100 94 100 1213 1146 .699 1.431 1.32 1.389 1.353 1.669 52 197 1.718 .78 80 3890 9290 49 57 273 281 0 797 184 612 1.227 743 559 .815 1.132 .295 .178
19 1104 1024 432 204 672 820 1125 960 437 222 693 756 0 0 270 408 87 104 100 100 100 96 1492 1449 .82 1.22 1.091 1.167 1.272 1.745 52 223 1.507 .82 80 4040 9280 48 56 288 296 0 878 175 703 1.046 823 648 .956 .935 .065 -.096
20 1748 1756 450 205 1298 1551 1767 1803 456 216 1317 1598 0 0 514 605 98 72 98 100 98 100 2849 2915 .837 1.195 1.213 1.225 1.266 1.534 52 251 1.321 .89 90 4170 9280 47 56 300 309 0 1506 176 1330 1.025 1546 1370 .976 1.04 .035 .057

Total number of rows: 43392

Table truncated, full table size 9436 Kbytes.




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