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Sample GSM91867 Query DataSets for GSM91867
Status Public on Jan 11, 2006
Title "003 Day2 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 "003 Day2 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "003 Day2 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/2001-10/21427.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 2236 2460 334 803 1902 1657 1376 1981 497 1054 1042 1178 0 0 1956 2183 565 1260 71 48 48 21 3559 2220 1.148 .871 1.131 .94 .787 3.921 52 357 .828 .54 90 1850 8930 28 37 41 50 0 1952 637 1315 .691 1572 935 1.446 .897 -.532 -.156
2 1124 2298 377 891 747 1407 1112 2103 414 957 735 1212 0 0 325 581 214 363 91 100 83 91 2154 1947 .531 1.884 1.649 1.972 1.934 1.73 12 90 2.202 .77 50 1980 8930 30 35 56 61 0 1824 707 1117 1.495 1669 962 .669 1.309 .58 .388
3 2839 3885 262 738 2577 3147 2261 3093 313 793 1999 2355 0 0 1847 2477 259 384 90 90 84 86 5724 4354 .819 1.221 1.178 1.243 1.249 1.461 52 285 1.293 .95 80 2130 8920 28 36 70 78 0 3083 586 2498 .969 2455 1869 1.032 .935 -.045 -.097
4 5611 2045 285 755 5326 1290 5040 1886 313 803 4755 1131 0 0 3271 1004 222 327 100 86 98 76 6616 5886 4.129 .242 .238 .238 .251 1.482 80 439 .26 .94 100 2300 8930 28 38 86 96 0 1623 599 1024 .192 1497 898 5.202 .189 -2.379 -2.405
5 830 1312 285 768 545 544 643 1095 363 800 358 327 0 0 647 866 453 254 38 53 17 33 1089 685 1.002 .998 .913 1.044 1.163 2.623 80 376 1.323 .85 100 2470 8940 29 39 103 113 -50 1041 610 432 .792 869 260 1.262 .725 -.336 -.464
6 7373 3360 293 871 7080 2489 5711 2752 345 999 5418 1881 0 0 6785 2191 255 453 91 85 84 72 9569 7299 2.845 .352 .347 .439 .339 2.261 120 528 .305 .89 130 2620 8930 26 39 116 129 0 2667 691 1975 .279 2184 1493 3.584 .276 -1.842 -1.86
7 453 1367 330 1296 123 71 351 1268 466 1349 21 -28 0 0 310 666 637 483 10 23 1 15 194 -7 1.732 .577 null 1.964 2.167 4.449 80 338 3.635 .51 100 2780 8940 29 39 134 144 -50 1085 1029 56 .458 1006 null 2.183 null -1.126 null
8 4467 3106 318 1239 4149 1867 2836 2201 347 1263 2518 962 0 0 4286 2332 155 346 96 61 93 57 6016 3480 2.222 .45 .382 .422 .491 2.527 80 443 .484 .92 110 2920 8920 26 37 147 158 0 2465 983 1482 .357 1747 763 2.8 .303 -1.485 -1.722
9 924 5017 338 1282 586 3735 959 4951 359 1425 621 3669 0 0 505 2636 158 534 76 88 67 82 4321 4290 .157 6.374 5.908 5.718 6.077 1.612 52 370 6.134 .89 90 3100 8940 29 38 166 175 -100 3982 1017 2964 5.059 3929 2912 .198 4.689 2.339 2.229
10 1413 4171 357 1247 1056 2924 1644 4468 376 1209 1287 3221 0 0 509 1344 160 379 100 91 83 91 3980 4508 .361 2.769 2.503 2.804 2.806 1.465 12 72 3.366 .89 50 3250 8910 28 33 183 188 -100 3310 990 2321 2.198 3546 2556 .455 1.986 1.136 .99
11 1767 5475 353 1042 1414 4433 1833 3777 388 1186 1480 2735 0 0 810 7888 167 711 83 83 83 83 5847 4215 .319 3.135 1.848 2.169 1.723 2.209 12 90 11.697 .43 50 3380 8930 30 35 196 201 -100 4345 827 3518 2.488 2998 2171 .402 1.467 1.315 .553
12 479 1386 293 926 186 460 333 1081 380 1001 40 155 0 0 398 1058 373 372 21 35 8 20 646 195 .404 2.473 3.875 2.668 3.051 3.507 80 459 33.598 .25 100 3560 8950 30 40 212 222 -50 1100 735 365 1.963 858 123 .509 3.075 .973 1.621
13 573 1294 281 888 292 406 427 1082 300 923 146 194 0 0 411 818 118 299 53 35 38 23 698 340 .719 1.39 1.329 1.579 1.856 2.738 80 349 2.334 .76 100 3720 8950 30 40 228 238 -50 1027 705 322 1.104 859 154 .906 1.055 .142 .077
14 2858 4113 282 889 2576 3224 1692 2582 309 920 1410 1693 0 0 2879 3829 151 260 93 82 88 77 5800 3103 .799 1.252 1.201 1.219 1.214 2.27 80 467 1.564 .86 110 3860 8920 26 37 241 252 0 3264 706 2559 .993 2049 1344 1.007 .953 -.01 -.07
15 1201 2952 287 855 914 2097 1195 3048 306 913 908 2193 0 0 585 1222 127 303 90 87 84 87 3011 3101 .436 2.294 2.415 2.415 2.447 2.2 32 138 2.367 .92 60 4050 8940 31 37 263 269 0 2343 679 1664 1.821 2419 1740 .549 1.917 .865 .939
16 2617 4373 275 812 2342 3561 1742 2905 278 822 1467 2093 0 0 2398 4071 101 199 95 91 92 85 5903 3560 .658 1.52 1.427 1.348 1.446 1.737 80 373 1.644 .97 100 4180 8930 28 38 274 284 0 3471 644 2826 1.207 2306 1661 .829 1.132 .271 .179
17 464 1030 270 796 194 234 365 867 289 801 95 71 0 0 318 553 145 196 42 40 22 25 428 166 .829 1.206 .747 1.902 2.18 3.253 80 375 2.047 .72 100 4340 8950 30 40 290 300 -50 817 632 186 .957 688 56 1.045 .593 -.063 -.754
18 495 1012 273 814 222 198 350 932 295 848 77 118 0 0 382 524 145 232 33 37 22 23 420 195 1.121 .892 1.532 1.66 1.358 4.338 80 329 1.556 .64 100 4500 8950 30 40 306 316 -50 803 646 157 .708 740 94 1.413 1.216 -.498 .282
19 1144 4467 293 883 851 3584 951 3650 320 998 658 2767 0 0 710 2663 146 498 86 93 71 82 4435 3425 .237 4.212 4.205 4.416 4.223 1.726 80 439 4.158 .92 110 4620 8930 27 38 317 328 -100 3545 701 2844 3.342 2897 2196 .299 3.337 1.741 1.739
20 422 936 283 845 139 91 331 869 303 924 48 24 0 0 272 388 136 396 30 13 17 8 230 72 1.527 .655 .5 1.592 1.557 2.482 80 379 2.085 .56 100 4810 8950 30 40 337 347 -50 743 671 72 .52 690 19 1.925 .397 -.945 -1.333

Total number of rows: 37632

Table truncated, full table size 8657 Kbytes.




Supplementary data files not provided
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