NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84183 Query DataSets for GSM84183
Status Public on Nov 19, 2005
Title 072801 Time Zero Z2 T-Cell
Sample type RNA
 
Channel 1
Source name 10 amplified MOATS pool
Organism Homo sapiens
Characteristics 10 amplified MOATS pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 072801 Time Zero Z2
Organism Homo sapiens
Characteristics 072801 Time Zero Z2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18916.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 Nov 17, 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 GPL3093
Series (1)
GSE3630 T-cell co-stimulation

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 3205 1515 176 281 3029 1234 3342 1434 182 298 3166 1153 0 0 1145 467 58 121 100 98 100 97 4263 4319 2.455 .407 .364 .414 .396 1.567 80 339 .37 .9 100 1620 9010 31 41 67 77 0 1918 356 1562 .516 1815 1459 1.939 .461 -.955 -1.117
2 780 923 198 324 582 599 755 862 223 341 557 538 0 0 199 274 114 161 100 100 91 83 1181 1095 .972 1.029 .966 .995 .92 1.69 12 46 1.119 .67 50 1770 8980 30 35 84 89 0 1168 410 758 1.303 1091 681 .768 1.223 .382 .29
3 1912 1848 180 293 1732 1555 1279 1253 188 308 1099 960 0 0 1539 1347 64 121 93 93 90 88 3287 2059 1.114 .898 .874 1.048 .947 2.768 80 411 .871 .87 110 1930 9000 29 40 97 108 0 2339 371 1968 1.136 1586 1215 .88 1.106 .185 .145
4 2063 1191 175 290 1888 901 1738 1015 186 311 1563 725 0 0 1326 619 65 124 98 97 97 90 2789 2288 2.095 .477 .464 .507 .468 1.949 80 347 .441 .9 100 2100 9000 30 40 115 125 0 1508 367 1141 .604 1285 918 1.655 .587 -.727 -.768
5 2454 1322 257 357 2197 965 2529 1445 303 363 2272 1088 0 0 585 373 158 148 100 100 100 100 3162 3360 2.277 .439 .479 .423 .507 1.606 12 52 .397 .79 50 2260 8990 31 36 133 138 0 1673 452 1222 .556 1829 1377 1.799 .606 -.847 -.722
6 10178 1043 179 298 9999 745 8361 898 231 311 8182 600 0 0 6608 539 422 125 98 90 96 82 10744 8782 13.421 .075 .073 .081 .075 1.859 52 288 .07 .85 90 2400 9000 30 39 145 154 0 1320 377 943 .094 1137 759 10.603 .093 -3.406 -3.429
7 205 328 171 310 34 18 165 305 210 319 -6 -5 0 0 127 143 374 136 3 18 0 2 52 -11 1.889 .529 null 1.741 2.099 3.419 80 365 4.332 .1 100 2570 9050 35 45 162 172 -50 415 392 23 .67 386 null 1.492 null -.577 null
8 7264 1545 163 321 7101 1224 7404 1407 189 343 7241 1086 0 0 3274 649 115 168 100 97 100 95 8325 8327 5.801 .172 .15 .168 .175 1.667 80 310 .162 .9 100 2720 9000 30 40 177 187 0 1956 406 1549 .218 1781 1375 4.583 .19 -2.196 -2.397
9 371 423 170 318 201 105 204 362 209 347 34 44 0 0 348 279 145 172 37 30 28 11 306 78 1.914 .522 1.294 1.361 1.318 4.055 80 414 .792 .74 100 2880 9060 36 46 193 203 -50 535 403 133 .661 458 56 1.512 1.638 -.597 .712
10 1504 1269 166 304 1338 965 1728 1248 181 324 1562 944 0 0 863 403 66 139 90 100 90 100 2303 2506 1.387 .721 .604 .934 .761 2.286 32 114 .607 .86 60 3040 9010 33 39 211 217 0 1606 385 1222 .913 1580 1195 1.095 .765 -.131 -.386
11 1252 988 171 306 1081 682 1270 940 196 335 1099 634 0 0 407 340 111 130 100 93 100 90 1763 1733 1.585 .631 .577 .574 .632 1.73 32 104 .641 .83 60 3190 9000 32 38 226 232 0 1251 387 863 .799 1190 803 1.252 .73 -.324 -.454
12 1038 1223 170 302 868 921 1067 1163 180 325 897 861 0 0 568 544 68 144 84 96 84 87 1789 1758 .942 1.061 .96 1.183 1.038 2.586 32 146 1.043 .78 70 3360 8990 30 37 242 249 0 1548 382 1166 1.343 1472 1090 .745 1.215 .426 .281
13 906 916 177 336 729 580 849 993 200 348 672 657 0 0 532 342 94 156 87 87 81 84 1309 1329 1.257 .796 .978 .883 .784 1.952 32 104 .039 .3 60 3500 9000 32 38 257 263 0 1159 425 734 1.007 1257 832 .993 1.238 .01 .308
14 1048 983 181 334 867 649 276 511 397 506 95 177 0 0 1703 1298 919 763 23 22 13 10 1516 272 1.336 .749 1.863 1.078 .9 3.029 80 450 .771 .94 100 3660 9060 36 46 271 281 -50 1244 423 822 .948 647 224 1.055 2.358 -.078 1.238
15 1047 946 183 324 864 622 1009 875 204 347 826 551 0 0 481 438 88 153 100 87 93 71 1486 1377 1.389 .72 .667 .673 .744 2.064 32 101 .739 .73 60 3800 9000 32 38 287 293 0 1197 410 787 .911 1108 697 1.097 .844 -.134 -.244
16 797 679 179 322 618 357 219 465 362 452 40 143 0 0 1410 613 746 504 25 28 10 11 975 183 1.731 .578 3.575 1.308 1 3.247 80 472 .544 .92 100 3970 9060 36 46 302 312 -50 859 408 452 .731 589 181 1.368 4.525 -.452 2.178
17 851 1043 204 389 647 654 825 996 212 408 621 607 0 0 359 238 96 150 91 100 91 100 1301 1228 .989 1.011 .977 .924 .968 1.436 12 52 .939 .77 50 4110 8990 31 36 318 323 0 1320 492 828 1.28 1261 768 .782 1.237 .356 .307
18 885 1260 188 325 697 935 946 1311 189 343 758 986 0 0 234 329 71 144 100 100 100 91 1632 1744 .745 1.341 1.301 1.322 1.412 1.69 12 52 1.339 .76 50 4270 8990 31 36 334 339 0 1595 411 1184 1.698 1659 1248 .589 1.647 .764 .719
19 1572 3077 174 307 1398 2770 1625 3457 177 321 1451 3150 0 0 794 1326 55 128 98 100 95 100 4168 4601 .505 1.981 2.171 2.15 1.935 1.873 80 384 2.008 .91 100 4430 9010 31 41 348 358 0 3895 389 3506 2.508 4376 3987 .399 2.748 1.327 1.458
20 726 1039 179 367 547 672 719 1030 178 386 540 663 0 0 148 268 45 136 100 100 100 100 1219 1203 .814 1.229 1.228 1.185 1.258 1.683 12 52 1.472 .67 50 4580 8990 31 36 365 370 0 1315 465 851 1.555 1304 839 .643 1.554 .637 .636

Total number of rows: 37632

Table truncated, full table size 8656 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap