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Sample GSM91862 Query DataSets for GSM91862
Status Public on Jan 11, 2006
Title "003 Day -4 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 Day -4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "003 Day -4 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/2001-10/21424.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 1575 1140 302 840 1273 300 1132 1006 316 856 830 166 0 0 1046 479 144 219 98 46 91 30 1573 996 4.243 .236 .2 .285 .276 2.254 80 515 .292 .58 110 1730 9230 29 40 28 39 0 1295 955 341 .268 1143 189 3.734 .227 -1.901 -2.138
2 782 1507 331 849 451 658 704 1483 334 871 373 634 0 0 282 432 119 317 93 81 71 46 1109 1007 .685 1.459 1.7 1.58 1.795 2.002 32 144 2.154 .68 60 1890 9200 29 35 47 53 0 1713 965 748 1.658 1685 720 .603 1.932 .729 .95
3 2172 2402 312 853 1860 1549 1776 2076 365 935 1464 1223 0 0 1319 1343 275 366 92 78 84 63 3409 2687 1.201 .833 .835 .751 .83 1.682 52 282 .933 .93 80 2030 9220 30 38 60 68 0 2730 969 1760 .946 2359 1390 1.057 .949 -.08 -.075
4 3748 1387 308 883 3440 504 3381 1341 361 937 3073 458 0 0 2039 563 281 336 97 58 96 33 3944 3531 6.825 .147 .149 .146 .17 2.082 80 406 .169 .76 100 2200 9210 28 38 76 86 0 1576 1003 573 .166 1524 520 6.006 .169 -2.586 -2.562
5 712 1191 296 904 416 287 546 1130 320 924 250 226 0 0 511 530 176 294 61 38 37 21 703 476 1.449 .69 .904 1.089 .897 3.156 80 353 1.178 .65 100 2370 9220 29 39 93 103 -50 1353 1027 326 .784 1284 257 1.276 1.027 -.351 .039
6 9346 2661 305 923 9041 1738 7220 2231 586 983 6915 1308 0 0 6842 1588 1499 373 90 76 78 69 10779 8223 5.202 .192 .189 .187 .205 1.539 52 307 .203 .96 90 2500 9210 28 37 106 115 0 3024 1049 1975 .218 2535 1486 4.578 .215 -2.195 -2.218
7 384 966 300 920 84 46 344 899 529 1008 44 -21 0 0 201 423 1324 484 0 18 0 3 130 23 1.826 .548 null 2.115 2.205 3.458 80 401 5.356 .33 100 2690 9220 29 39 125 135 -50 1098 1045 52 .622 1022 null 1.607 null -.684 null
8 4573 1896 286 910 4287 986 4382 1857 296 950 4096 947 0 0 2143 688 105 291 98 83 98 75 5273 5043 4.348 .23 .231 .233 .248 2.128 80 425 .227 .75 110 2820 9210 27 38 137 148 0 2155 1034 1120 .261 2110 1076 3.826 .263 -1.936 -1.928
9 720 2412 299 906 421 1506 748 2587 324 951 449 1681 0 0 413 1303 138 280 71 71 68 71 1927 2130 .28 3.577 3.744 3.214 3.642 1.745 32 208 3.677 .83 70 2970 9230 31 38 154 161 0 2741 1030 1711 4.065 2940 1910 .246 4.254 2.023 2.089
10 559 1350 303 908 256 442 408 1067 316 931 105 159 0 0 335 787 126 250 45 40 37 27 698 264 .579 1.727 1.514 2.011 2.352 3.939 80 411 2.685 .76 100 3160 9210 28 38 172 182 -50 1534 1032 502 1.962 1213 181 .51 1.721 .972 .783
11 1305 1933 297 934 1008 999 1397 1974 348 992 1100 1040 0 0 466 751 165 324 90 81 87 75 2007 2140 1.009 .991 .945 .964 1.07 1.619 32 139 1.315 .88 60 3280 9220 31 37 186 192 0 2197 1061 1135 1.126 2243 1182 .888 1.074 .171 .104
12 848 2036 329 1016 519 1020 863 2080 332 1057 534 1064 0 0 170 355 115 267 100 100 91 91 1539 1598 .509 1.965 1.993 1.972 1.95 1.625 12 90 2.683 .73 50 3460 9200 29 34 204 209 0 2314 1155 1159 2.233 2364 1209 .448 2.264 1.159 1.179
13 505 1171 310 1049 195 122 427 1082 343 1088 117 33 0 0 255 546 265 346 32 25 12 17 317 150 1.598 .626 .282 1.995 2.21 4.258 80 422 2.779 .55 100 3630 9210 28 38 219 229 -50 1331 1192 139 .711 1230 38 1.407 .321 -.492 -1.642
14 3966 3789 321 1024 3645 2765 3869 3900 508 1147 3548 2876 0 0 2286 1820 596 488 96 87 84 78 6410 6424 1.318 .759 .811 .715 .752 1.488 32 200 .787 .95 70 3770 9200 28 35 234 241 0 4306 1164 3142 .862 4432 3268 1.16 .921 -.214 -.119
15 601 1270 297 884 304 386 522 1118 392 932 225 234 0 0 410 696 395 530 23 31 8 20 690 459 .788 1.27 1.04 1.555 1.601 2.571 80 450 2.126 .72 100 3940 9210 28 38 250 260 -50 1443 1005 439 1.443 1270 266 .693 1.182 .529 .241
16 3539 5440 156 296 3383 5144 2543 3641 321 667 2387 3345 0 0 2698 4131 515 823 90 90 81 87 8527 5732 .658 1.521 1.401 1.647 1.521 1.557 32 134 1.517 .99 60 4100 9180 27 33 268 274 -100 6182 336 5845 1.728 4138 3801 .579 1.592 .789 .671
17 237 570 240 630 -3 -60 187 585 242 586 -53 -45 0 0 196 415 161 368 18 15 3 3 -63 -98 null null null 2.143 2.744 2.672 80 427 2.937 .75 100 4260 9210 28 38 282 292 -100 648 716 -68 null 665 null null null null null
18 506 920 273 759 233 161 443 801 280 758 170 42 0 0 305 415 125 322 52 25 36 15 394 212 1.447 .691 .247 1.161 1.081 4.336 80 337 2.92 .42 100 4420 9210 28 38 298 308 -50 1045 863 183 .785 910 48 1.274 .281 -.349 -1.833
19 1016 3356 274 756 742 2600 924 2947 284 799 650 2191 0 0 448 1669 109 259 97 98 90 97 3342 2841 .285 3.504 3.371 3.417 3.623 1.517 80 362 3.696 .93 100 4560 9200 27 37 312 322 0 3814 859 2955 3.982 3349 2490 .251 3.83 1.993 1.938
20 443 888 273 733 170 155 363 786 295 792 90 53 0 0 270 402 159 349 36 30 22 11 325 143 1.097 .912 .589 1.576 1.569 4.099 80 405 2.45 .51 100 4730 9210 28 38 329 339 -50 1009 833 176 1.036 893 60 .965 .669 .051 -.58

Total number of rows: 37632

Table truncated, full table size 8694 Kbytes.




Supplementary data files not provided
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