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Sample GSM91869 Query DataSets for GSM91869
Status Public on Jan 11, 2006
Title "003 Day6 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 Day6 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "003 Day6 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/2001-10/21429.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 2525 1658 275 782 2250 876 1875 1261 293 825 1600 479 0 0 2106 1089 115 273 93 63 91 45 3126 2079 2.568 .389 .299 .412 .417 2.488 80 409 .433 .87 100 2220 9130 46 56 60 70 0 1863 879 984 .437 1417 538 2.286 .336 -1.193 -1.572
2 1347 2347 347 757 1000 1590 1391 2193 362 807 1044 1436 0 0 341 723 133 316 100 100 91 91 2590 2480 .629 1.59 1.375 1.519 1.464 1.528 12 90 1.921 .87 50 2390 9120 47 52 79 84 0 2637 851 1787 1.787 2464 1613 .56 1.545 .837 .628
3 2668 3389 291 648 2377 2741 2000 2590 346 708 1709 1942 0 0 1995 2335 276 329 88 86 82 84 5118 3651 .867 1.153 1.136 1.072 1.126 2.122 52 341 1.125 .94 90 2530 9120 45 54 91 100 0 3808 728 3080 1.296 2910 2182 .772 1.277 .374 .353
4 4983 2056 308 527 4675 1529 4376 1755 362 594 4068 1228 0 0 2862 1001 266 297 98 96 97 85 6204 5296 3.058 .327 .302 .332 .311 1.613 80 446 .32 .92 100 2690 9120 45 55 107 117 0 2310 592 1718 .367 1972 1380 2.721 .339 -1.444 -1.56
5 950 1164 297 540 653 624 670 816 329 559 373 276 0 0 759 889 170 174 72 63 55 41 1277 649 1.046 .956 .74 1.05 1.061 2.919 80 358 1.153 .85 100 2880 9140 47 57 126 136 -50 1308 607 701 1.074 917 310 .931 .831 .103 -.266
6 8916 4307 269 649 8647 3658 6594 3268 272 686 6325 2619 0 0 6487 2714 92 230 100 96 100 93 12305 8944 2.364 .423 .414 .419 .407 1.633 80 358 .39 .96 100 3010 9120 45 55 139 149 0 4839 729 4110 .475 3672 2943 2.104 .465 -1.073 -1.104
7 383 903 264 757 119 146 327 786 301 785 63 29 0 0 258 501 286 253 12 27 8 16 265 92 .815 1.227 .46 1.614 1.836 2.944 80 369 3.497 .48 100 3190 9140 47 57 157 167 -50 1015 851 164 1.379 883 33 .725 .517 .463 -.951
8 4405 1901 263 744 4142 1157 2698 1335 284 794 2435 591 0 0 4085 1415 124 337 96 66 93 45 5299 3026 3.58 .279 .243 .264 .284 2.295 80 403 .301 .91 100 3330 9120 45 55 171 181 0 2136 836 1300 .314 1500 664 3.186 .273 -1.672 -1.875
9 1117 2657 293 717 824 1940 1114 2622 340 890 821 1905 0 0 254 551 185 557 100 100 100 100 2764 2726 .425 2.354 2.32 2.368 2.465 1.38 12 98 2.503 .85 50 3510 9130 48 53 191 196 0 2985 806 2180 2.645 2946 2140 .378 2.607 1.403 1.382
10 1401 2902 286 718 1115 2184 1455 2846 315 741 1169 2128 0 0 312 675 134 249 100 100 100 100 3299 3297 .511 1.959 1.82 1.958 1.951 1.301 12 80 2.192 .91 50 3630 9110 46 51 203 208 0 3261 807 2454 2.201 3198 2391 .454 2.045 1.138 1.032
11 1291 1885 286 550 1005 1335 1292 1776 299 594 1006 1226 0 0 583 819 112 220 96 93 90 87 2340 2232 .753 1.328 1.219 1.309 1.225 2.276 32 164 1.425 .86 60 3820 9140 49 55 222 228 0 2118 618 1500 1.493 1996 1378 .67 1.369 .578 .453
12 835 1641 270 530 565 1111 779 1624 288 568 509 1094 0 0 342 621 117 195 90 96 78 81 1676 1603 .509 1.966 2.149 2.227 1.862 2.277 32 134 2.034 .84 60 3970 9110 46 52 237 243 0 1844 596 1248 2.209 1825 1229 .453 2.415 1.144 1.272
13 819 2144 259 540 560 1604 863 2161 279 563 604 1621 0 0 430 733 108 175 78 96 75 96 2164 2225 .349 2.864 2.684 3.079 2.223 2.724 32 210 3.296 .68 70 4130 9130 47 54 252 259 0 2409 607 1802 3.218 2428 1821 .311 3.015 1.686 1.592
14 3136 4774 251 583 2885 4191 2075 3514 270 624 1824 2931 0 0 2953 4316 128 224 92 91 85 82 7076 4755 .688 1.453 1.607 1.426 1.395 2.07 80 442 1.478 .94 100 4270 9120 45 55 265 275 0 5364 655 4709 1.632 3948 3293 .613 1.806 .707 .852
15 1352 2408 296 689 1056 1719 1397 2443 319 711 1101 1754 0 0 333 554 143 259 100 100 100 100 2775 2855 .614 1.628 1.593 1.63 1.572 1.478 12 71 1.843 .87 50 4460 9120 47 52 286 291 0 2706 774 1931 1.829 2745 1971 .547 1.79 .871 .84
16 3414 7525 238 765 3176 6760 2173 4433 316 844 1935 3668 0 0 2569 6080 378 744 94 92 88 86 9936 5603 .47 2.128 1.896 1.956 2.098 1.514 52 328 2.296 .97 90 4560 9110 44 53 294 303 0 8455 860 7596 2.392 4981 4121 .418 2.13 1.258 1.091
17 263 487 227 698 36 -211 133 206 290 731 -94 -492 0 0 362 619 334 692 12 6 2 1 -175 -586 null null null 3.192 3.677 2.725 80 429 2.619 .76 100 4750 9140 47 57 313 323 -50 547 784 -237 null 231 null null null null null
18 409 874 230 832 179 42 301 835 254 804 71 3 0 0 412 676 168 497 35 21 22 11 221 74 4.262 .235 .042 2.478 2.899 2.834 80 365 2.573 .76 100 4900 9140 47 57 328 338 -50 982 935 47 .264 938 3 3.793 .047 -1.923 -4.397
19 1016 2466 252 925 764 1541 885 1934 281 937 633 1009 0 0 596 1458 172 455 80 68 67 53 2305 1642 .496 2.017 1.594 1.925 2.004 2.26 80 378 2.386 .89 100 5060 9140 47 57 344 354 -50 2771 1039 1731 2.266 2173 1134 .441 1.791 1.18 .841
20 447 1363 281 957 166 406 334 1218 296 1034 53 261 0 0 328 667 187 420 27 38 16 21 572 314 .409 2.446 4.925 2.362 2.715 3.453 80 392 3.596 .55 100 5220 9140 47 57 360 370 -50 1531 1075 456 2.748 1369 293 .364 5.533 1.458 2.468

Total number of rows: 37632

Table truncated, full table size 8653 Kbytes.




Supplementary data files not provided
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