NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91828 Query DataSets for GSM91828
Status Public on Jan 11, 2006
Title "083 Day4 in-vivo SP Inf, PBMC 3rd TC"
Sample type RNA
 
Channel 1
Source name "CRG, 1 round of amplification, Addie and Kate from 7/19/01"
Organism Homo sapiens
Characteristics "CRG, 1 round of amplification, Addie and Kate from 7/19/01"
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name "083 Day4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "083 Day4 in-vivo SP Inf, PBMC 3rd TC"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21413.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 Jan 10, 2006
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)
GSE4013 Host response to smallpox

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 1067 1105 203 592 864 513 798 1033 215 604 595 441 0 0 690 447 131 160 93 80 85 62 1377 1036 1.684 .594 .741 .594 .631 2.297 80 490 .593 .83 110 1880 9440 28 39 49 60 0 722 387 335 .388 675 288 2.577 .484 -1.366 -1.046
2 474 1372 212 663 262 709 491 1313 235 679 279 650 0 0 122 319 104 212 91 91 58 91 971 929 .37 2.706 2.33 2.712 2.861 1.883 12 98 2.927 .73 50 2030 9420 29 34 67 72 0 897 433 463 1.769 858 425 .565 1.523 .823 .607
3 1165 2373 202 602 963 1771 1077 2244 366 660 875 1642 0 0 673 1242 3033 910 0 63 0 46 2734 2517 .544 1.839 1.877 1.84 1.876 2.009 80 446 .338 .8 100 2200 9430 28 38 82 92 0 1551 393 1158 1.202 1467 1073 .832 1.227 .265 .295
4 2333 1704 199 658 2134 1046 2173 1594 210 673 1974 936 0 0 1118 657 84 162 100 90 100 85 3180 2910 2.04 .49 .474 .445 .476 1.709 80 457 .502 .93 110 2370 9430 27 38 98 109 0 1114 430 684 .32 1042 612 3.121 .31 -1.642 -1.69
5 608 992 201 733 407 259 298 859 222 753 97 126 0 0 1615 633 118 181 43 37 25 17 666 223 1.571 .636 1.299 1.294 1.176 3.881 80 431 .386 .82 100 2560 9420 27 37 118 128 -50 648 479 169 .416 561 82 2.404 .849 -1.266 -.236
6 4468 1990 202 789 4266 1201 3704 1622 254 817 3502 833 0 0 2806 961 379 204 98 92 94 82 5467 4335 3.552 .282 .238 .263 .276 1.398 52 237 .285 .94 90 2670 9430 28 37 129 138 0 1301 516 785 .184 1060 544 5.435 .155 -2.442 -2.685
7 293 1012 219 866 74 146 276 945 269 889 57 79 0 0 125 330 291 212 4 32 0 13 220 136 .507 1.973 1.386 1.838 2.054 4.268 120 451 .866 .43 120 2820 9420 26 38 143 155 0 661 566 95 1.29 618 52 .775 .906 .367 -.143
8 1649 2007 227 852 1422 1155 847 1396 257 876 620 544 0 0 1622 1369 225 199 70 71 55 55 2577 1164 1.231 .812 .877 .903 .868 2.181 120 435 .804 .92 120 2970 9420 26 38 158 170 0 1312 557 755 .531 912 356 1.884 .573 -.914 -.802
9 669 1872 215 771 454 1101 367 1420 226 799 152 649 0 0 1801 2288 88 186 71 80 45 64 1555 801 .412 2.425 4.27 3.29 3.668 2.755 120 497 1.381 .93 120 3130 9420 26 38 174 186 0 1224 504 720 1.585 928 424 .631 2.791 .665 1.481
10 402 1399 210 719 192 680 380 1291 304 781 170 572 0 0 171 491 855 609 0 47 0 15 872 742 .282 3.542 3.365 3.624 3.71 2.091 80 481 .979 .89 110 3300 9420 26 37 191 202 0 914 470 444 2.315 844 374 .432 2.199 1.211 1.137
11 671 1659 211 716 460 943 587 1615 256 775 376 899 0 0 258 345 152 290 96 96 71 87 1403 1275 .488 2.05 2.391 2.19 2.246 1.492 32 164 2.01 .82 60 3440 9430 30 36 208 214 0 1084 468 616 1.34 1056 588 .746 1.563 .422 .644
12 500 1732 218 818 282 914 484 1805 238 873 266 987 0 0 193 428 102 247 84 90 62 81 1196 1253 .309 3.241 3.711 3.592 3.636 1.801 32 220 3.639 .71 70 3610 9400 26 33 224 231 0 1132 535 597 2.118 1180 645 .472 2.425 1.083 1.278
13 454 1108 212 772 242 336 337 991 252 814 125 219 0 0 702 845 305 342 18 38 3 15 578 344 .72 1.388 1.752 2.28 2.148 2.979 80 400 1.169 .87 100 3820 9420 27 37 244 254 -50 724 505 220 .907 648 143 1.102 1.145 -.14 .195
14 1566 3234 192 737 1374 2497 1466 2970 212 757 1274 2233 0 0 1050 1856 176 208 89 95 78 90 3871 3507 .55 1.817 1.753 1.949 1.864 1.931 120 488 1.851 .93 120 3950 9420 26 38 256 268 0 2114 482 1632 1.188 1941 1459 .842 1.146 .248 .196
15 412 1440 188 707 224 733 379 1268 199 713 191 561 0 0 192 593 76 165 74 88 58 75 957 752 .306 3.272 2.937 3.322 3.208 2.739 120 464 3.861 .78 120 4110 9420 26 38 272 284 0 941 462 479 2.139 829 367 .468 1.92 1.097 .941
16 1358 2849 197 650 1161 2199 1119 2568 205 660 922 1918 0 0 888 1562 79 156 95 100 93 92 3360 2840 .528 1.894 2.08 2.105 1.936 2.094 120 494 1.908 .92 120 4270 9420 26 38 288 300 0 1862 425 1437 1.238 1678 1254 .808 1.36 .308 .443
17 321 1119 197 668 124 451 313 1137 209 686 116 469 0 0 104 312 121 166 46 75 15 62 575 585 .275 3.637 4.043 3.044 3.979 2.716 32 205 5.845 .47 70 4420 9410 27 34 305 312 0 731 437 295 2.377 743 307 .421 2.643 1.249 1.402
18 291 817 194 635 97 182 285 779 210 664 91 144 0 0 124 259 181 243 20 37 5 13 279 235 .533 1.876 1.582 2.149 2.203 3.341 80 386 2.787 .42 100 4600 9410 26 36 322 332 -50 534 415 119 1.226 509 94 .815 1.034 .294 .049
19 566 2446 181 626 385 1820 560 2469 201 657 379 1843 0 0 278 1169 166 235 68 96 56 85 2205 2222 .212 4.727 4.863 4.917 4.774 1.921 80 403 4.437 .79 110 4730 9410 25 36 334 345 0 1599 409 1190 3.09 1614 1205 .324 3.178 1.627 1.668
20 264 767 180 624 84 143 224 702 191 646 44 78 0 0 131 287 67 172 43 37 25 25 227 122 .587 1.702 1.773 2.761 2.294 3.26 80 405 4.133 .48 100 4910 9410 26 36 353 363 -50 501 408 93 1.113 459 51 .899 1.159 .154 .212

Total number of rows: 37632

Table truncated, full table size 8606 Kbytes.




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