NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91848 Query DataSets for GSM91848
Status Public on Jan 11, 2006
Title "099 Day9 in-vivo SP Inf, PBMC 1st TC, relabel"
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 "099 Day9 in-vivo SP Inf, PBMC 1st TC, relabel"
Organism Homo sapiens
Characteristics "099 Day9 in-vivo SP Inf, PBMC 1st TC, relabel"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19504.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 GPL3346
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 4493 5655 172 514 4321 5141 4610 5440 195 543 4438 4926 0 0 930 1661 98 211 100 100 100 100 9462 9364 .84 1.19 1.11 1.154 1.201 1.337 80 473 1.243 .94 110 1420 9380 80 91 68 79 0 5004 455 4550 1.053 4814 4359 .95 .982 .074 -.026
2 1541 4036 173 506 1368 3530 1615 3997 200 528 1442 3491 0 0 383 1224 108 225 100 100 100 100 4898 4933 .388 2.58 2.421 2.513 2.577 1.31 80 380 2.813 .95 100 1580 9380 81 91 85 95 0 3572 448 3124 2.284 3537 3089 .438 2.142 1.191 1.099
3 4811 7314 168 447 4643 6867 5029 7460 186 474 4861 7013 0 0 1203 1610 95 201 100 100 100 100 11510 11874 .676 1.479 1.443 1.514 1.483 1.282 80 413 1.476 .96 110 1740 9390 81 92 100 111 0 6473 396 6077 1.309 6602 6206 .764 1.277 .388 .352
4 7872 3385 171 454 7701 2931 8305 3467 181 473 8134 3013 0 0 1872 878 76 190 100 100 100 100 10632 11147 2.627 .381 .37 .374 .383 1.262 80 379 .376 .95 100 1900 9380 81 91 117 127 0 2996 402 2594 .337 3068 2666 2.969 .328 -1.57 -1.609
5 5163 4974 174 462 4989 4512 5251 4632 184 489 5077 4170 0 0 2543 2246 68 179 100 100 100 100 9501 9247 1.106 .904 .821 .923 .973 1.432 80 378 .9 .96 100 2060 9380 81 91 133 143 0 4402 409 3993 .8 4099 3690 1.249 .727 -.321 -.46
6 36339 13367 174 488 36165 12879 35102 13469 179 506 34928 12981 0 0 7799 3970 56 190 100 100 100 100 49044 47909 2.808 .356 .372 .344 .36 1.285 80 480 .359 .97 110 2220 9380 80 91 148 159 0 11829 432 11397 .315 11919 11488 3.173 .329 -1.666 -1.604
7 1907 4397 180 519 1727 3878 1855 4956 189 524 1675 4437 0 0 880 2199 56 181 100 100 100 96 5605 6112 .445 2.246 2.649 2.017 2.26 1.567 32 213 2.443 .95 70 2370 9380 82 89 165 172 0 3891 459 3432 1.987 4386 3927 .503 2.344 .991 1.229
8 7450 10582 168 514 7282 10068 7740 10955 202 553 7572 10441 0 0 2372 3251 140 232 100 100 100 100 17350 18013 .723 1.383 1.379 1.405 1.367 1.282 80 493 1.398 .97 110 2530 9380 80 91 179 190 0 9365 455 8910 1.224 9695 9240 .817 1.22 .291 .287
9 1876 7428 175 518 1701 6910 1890 7578 190 540 1715 7060 0 0 450 1853 94 214 100 100 100 100 8611 8775 .246 4.062 4.117 4.061 4.108 1.267 80 378 4.282 .95 100 2690 9380 81 91 196 206 0 6573 458 6115 3.595 6706 6248 .278 3.643 1.846 1.865
10 3751 9156 171 501 3580 8655 3709 9375 174 529 3538 8874 0 0 1437 3680 46 206 100 100 100 100 12235 12412 .414 2.418 2.508 2.382 2.385 1.373 80 378 2.52 .96 100 2850 9380 81 91 212 222 0 8103 443 7659 2.139 8296 7853 .467 2.22 1.097 1.15
11 2255 4173 169 482 2086 3691 2131 3975 174 509 1962 3493 0 0 801 1475 44 195 100 100 100 100 5777 5455 .565 1.769 1.78 1.747 1.765 1.313 80 366 1.838 .95 100 3010 9380 81 91 228 238 0 3693 427 3266 1.566 3518 3091 .639 1.576 .647 .656
12 2888 6954 168 498 2720 6456 2788 6602 172 518 2620 6104 0 0 1067 2641 48 214 100 100 100 100 9176 8724 .421 2.374 2.33 2.362 2.405 1.22 80 366 2.44 .97 100 3160 9380 81 91 243 253 0 6154 441 5713 2.1 5842 5402 .476 2.062 1.071 1.044
13 2745 7603 175 503 2570 7100 2880 7384 181 519 2705 6881 0 0 727 2042 60 193 100 100 100 100 9670 9586 .362 2.763 2.544 2.754 2.919 1.253 52 332 2.818 .96 90 3310 9380 81 90 258 267 0 6728 445 6283 2.445 6535 6089 .409 2.251 1.29 1.171
14 7094 12361 167 497 6927 11864 7036 12475 175 519 6869 11978 0 0 1257 2674 59 184 100 100 100 100 18791 18847 .584 1.713 1.744 1.695 1.704 1.174 80 454 1.743 .97 110 3480 9380 80 91 274 285 0 10939 440 10499 1.516 11040 10600 .66 1.543 .6 .626
15 2354 5540 168 538 2186 5002 2338 5293 182 587 2170 4755 0 0 677 1644 86 343 100 100 100 100 7188 6925 .437 2.288 2.191 2.281 2.33 1.258 80 352 2.387 .96 100 3630 9380 81 91 290 300 0 4903 476 4427 2.025 4684 4208 .494 1.939 1.018 .955
16 7053 41298 175 605 6878 40693 7702 44466 206 720 7527 43861 0 0 2352 14363 147 574 100 100 100 100 47571 51388 .169 5.916 5.827 5.933 6.085 1.237 80 442 6.029 .98 110 3780 9380 80 91 304 315 0 36547 535 36012 5.236 39350 38815 .191 5.157 2.388 2.366
17 1731 4433 179 570 1552 3863 1711 4565 211 653 1532 3995 0 0 541 1336 133 439 100 100 100 100 5415 5527 .402 2.489 2.608 2.503 2.443 1.319 52 335 2.545 .95 90 3930 9370 80 89 320 329 0 3923 504 3419 2.203 4040 3535 .454 2.308 1.139 1.206
18 1667 3635 179 536 1488 3099 1665 3551 192 579 1486 3015 0 0 386 792 82 249 100 100 100 100 4587 4501 .48 2.083 2.029 2.081 2.115 1.271 52 272 2.12 .94 80 4100 9380 82 90 338 346 0 3217 474 2742 1.843 3142 2668 .543 1.796 .882 .844
19 2284 10063 180 555 2104 9508 2334 10476 191 601 2154 9921 0 0 591 2253 67 265 100 100 100 100 11612 12075 .221 4.519 4.606 4.62 4.463 1.271 80 370 4.499 .96 100 4250 9380 81 91 352 362 0 8905 491 8414 3.999 9271 8780 .25 4.076 2 2.027
20 969 1739 184 524 785 1215 1006 1634 190 550 822 1110 0 0 243 480 53 216 98 98 98 98 2000 1932 .646 1.548 1.35 1.553 1.474 1.491 80 369 1.735 .89 100 4410 9380 81 91 368 378 0 1539 464 1075 1.37 1446 982 .73 1.195 .454 .257

Total number of rows: 37632

Table truncated, full table size 8663 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.