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Sample GSM91810 Query DataSets for GSM91810
Status Public on Jan 11, 2006
Title "083 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 "083 Day -4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "083 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/2001-10/21409.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 1046 714 119 282 927 432 793 625 129 287 674 343 0 0 746 404 79 81 92 85 91 73 1359 1017 2.146 .466 .509 .475 .48 1.852 80 398 .468 .88 110 2000 9300 69 80 59 70 0 425 168 257 .277 372 204 3.605 .303 -1.85 -1.723
2 252 614 123 281 129 333 246 602 135 301 123 321 0 0 99 194 65 111 67 86 46 73 462 444 .387 2.581 2.61 2.938 2.799 2.973 52 279 2.994 .66 80 2150 9270 68 76 76 84 0 365 167 198 1.537 358 191 .651 1.553 .62 .635
3 1082 1966 119 266 963 1700 984 1819 127 280 865 1553 0 0 674 1079 53 93 97 98 92 97 2663 2418 .566 1.765 1.795 1.921 1.845 1.634 80 450 1.743 .95 110 2320 9290 68 79 91 102 0 1170 158 1012 1.051 1083 924 .952 1.069 .071 .096
4 2098 1131 119 258 1979 873 2184 1163 132 271 2065 905 0 0 924 454 76 94 96 93 96 92 2852 2970 2.267 .441 .438 .476 .461 1.537 80 452 .437 .93 110 2470 9280 67 78 106 117 0 673 154 520 .263 692 539 3.808 .261 -1.929 -1.939
5 198 399 128 250 70 149 159 352 140 266 31 102 0 0 122 190 78 99 37 50 20 26 219 133 .47 2.129 3.29 1.939 1.878 3.892 80 386 1.355 .75 100 2670 9290 69 79 127 137 -50 238 149 89 1.267 210 61 .789 1.959 .341 .97
6 3986 1733 123 265 3863 1468 3737 1600 168 298 3614 1335 0 0 2056 697 593 324 100 97 90 92 5331 4949 2.631 .38 .369 .397 .382 1.429 80 456 .351 .95 110 2790 9290 68 79 138 149 0 1032 158 874 .226 952 795 4.421 .22 -2.144 -2.185
7 163 370 125 276 38 94 153 349 146 282 28 73 0 0 74 151 104 73 18 50 3 26 132 101 .404 2.474 2.607 2.059 2.042 3.43 80 362 3.379 .41 100 2990 9290 69 79 159 169 -50 220 164 56 1.472 208 43 .679 1.552 .558 .634
8 1598 1130 123 281 1475 849 1355 986 134 287 1232 705 0 0 1242 711 66 78 98 93 93 88 2324 1937 1.737 .576 .572 .589 .588 2.202 120 496 .552 .93 120 3100 9290 68 80 169 181 0 673 167 505 .343 587 420 2.919 .341 -1.545 -1.554
9 255 944 144 313 111 631 231 782 176 350 87 469 0 0 122 452 333 213 4 92 0 53 742 556 .176 5.685 5.391 5.615 5.171 2.255 120 529 2.471 .28 120 3270 9290 68 80 186 198 0 562 186 376 3.384 465 279 .296 3.209 1.759 1.682
10 2186 4731 158 324 2028 4407 1203 2157 168 362 1045 1833 0 0 2446 4917 73 152 96 100 87 96 6435 2878 .46 2.173 1.754 2.326 2.22 1.964 32 175 2.203 .89 70 3410 9320 73 80 202 209 -100 2816 193 2623 1.293 1284 1091 .773 1.044 .371 .062
11 347 691 132 286 215 405 264 617 148 307 132 331 0 0 208 309 105 121 57 81 38 63 620 463 .531 1.884 2.508 2.193 1.865 2.146 80 465 1.812 .78 110 3570 9290 68 79 216 227 0 411 170 241 1.121 367 197 .892 1.493 .165 .578
12 222 603 127 273 95 330 209 575 140 296 82 302 0 0 80 149 96 163 40 90 16 43 425 384 .288 3.474 3.683 3.631 3.525 2.181 80 485 2.839 .59 110 3730 9290 68 79 232 243 0 359 163 196 2.068 342 180 .484 2.192 1.048 1.132
13 211 426 118 259 93 167 184 375 128 269 66 116 0 0 113 180 65 80 50 67 28 40 260 182 .557 1.796 1.758 1.992 1.961 2.726 80 388 1.786 .63 100 3930 9290 69 79 253 263 -50 254 154 99 1.069 223 69 .936 1.046 .096 .065
14 1249 2275 111 259 1138 2016 1063 2119 118 264 952 1860 0 0 738 1254 54 70 97 100 96 98 3154 2812 .564 1.772 1.954 1.913 1.728 1.759 80 417 1.778 .95 110 4040 9290 68 79 263 274 0 1354 154 1200 1.054 1261 1107 .948 1.163 .077 .218
15 272 753 108 267 164 486 258 695 123 279 150 428 0 0 139 381 92 91 69 82 40 75 650 578 .337 2.963 2.853 2.722 2.746 2.791 52 312 3.081 .53 90 4210 9300 70 79 281 290 0 448 159 289 1.764 414 255 .567 1.698 .819 .764
16 1081 2740 108 272 973 2468 1003 2355 126 288 895 2083 0 0 594 1585 102 115 96 100 93 98 3441 2978 .394 2.536 2.327 2.463 2.439 1.461 80 413 2.641 .93 110 4360 9300 69 80 295 306 0 1631 162 1469 1.51 1402 1240 .662 1.385 .594 .47
17 207 620 110 305 97 315 209 553 118 327 99 248 0 0 78 213 47 113 67 90 51 55 412 347 .308 3.247 2.505 3 2.846 2.775 52 265 5.027 .48 80 4500 9300 71 79 311 319 0 369 182 188 1.933 329 148 .517 1.491 .951 .576
18 209 582 118 349 91 233 158 503 124 361 40 154 0 0 152 339 52 111 45 62 28 37 324 194 .391 2.56 3.85 2.639 2.562 3.326 80 375 2.755 .7 100 4710 9290 69 79 331 341 -50 346 208 139 1.524 299 92 .656 2.292 .608 1.196
19 568 2751 124 400 444 2351 512 2577 131 409 388 2177 0 0 218 1128 60 107 97 100 95 100 2795 2565 .189 5.295 5.611 5.428 5.629 1.504 80 387 5.633 .91 110 4830 9290 68 79 342 353 0 1638 238 1399 3.152 1534 1296 .317 3.34 1.656 1.74
20 214 629 127 420 87 209 188 577 132 430 61 157 0 0 115 247 54 114 53 62 28 35 296 218 .416 2.402 2.574 2.288 2.027 3.345 80 375 2.659 .65 100 5020 9290 69 79 362 372 -50 374 250 124 1.43 343 93 .699 1.532 .516 .615

Total number of rows: 37632

Table truncated, full table size 8522 Kbytes.




Supplementary data files not provided

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