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Sample GSM91709 Query DataSets for GSM91709
Status Public on Jan 11, 2006
Title "282 Day11 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 "282 Day11 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "282 Day11 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/2001-10/21504.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 1511 612 165 354 1346 258 1071 580 172 376 906 226 0 0 1045 254 77 166 98 60 96 40 1604 1132 5.217 .192 .249 .24 .213 2.969 80 480 .168 .49 110 1760 9760 58 69 32 43 0 1093 632 461 .342 1036 404 2.922 .445 -1.547 -1.167
2 232 403 154 325 78 78 194 364 163 343 40 39 0 0 139 174 75 144 42 32 22 12 156 79 1 1 .975 1.45 1.44 3.635 80 355 3.502 .23 100 1950 9780 61 71 52 62 -50 720 580 139 1.786 650 70 .56 1.741 .837 .8
3 1717 1207 152 336 1565 871 1229 962 155 345 1077 626 0 0 1274 739 66 139 95 86 93 78 2436 1703 1.797 .557 .581 .59 .597 2.444 80 334 .558 .9 100 2070 9760 59 69 64 74 0 2155 600 1555 .994 1718 1118 1.006 1.038 -.009 .054
4 3126 918 157 329 2969 589 2771 854 166 341 2614 525 0 0 1904 415 77 146 98 86 98 70 3558 3139 5.041 .198 .201 .177 .197 1.949 80 407 .189 .83 100 2230 9750 58 68 80 90 0 1639 588 1052 .354 1525 938 2.823 .359 -1.497 -1.479
5 487 446 160 336 327 110 298 412 173 355 138 76 0 0 549 211 86 166 57 30 45 12 437 214 2.973 .336 .551 .722 .701 3.549 80 353 .294 .43 100 2420 9780 61 71 99 109 -50 796 600 196 .601 736 136 1.665 .983 -.735 -.024
6 8096 1181 146 328 7950 853 7515 1101 164 349 7369 773 0 0 5199 577 81 163 100 88 100 75 8803 8142 9.32 .107 .105 .099 .105 2.016 80 363 .101 .9 100 2550 9750 58 68 112 122 0 2109 586 1523 .192 1966 1380 5.219 .187 -2.384 -2.416
7 213 366 141 314 72 52 182 316 162 340 41 2 0 0 136 275 126 153 27 18 7 6 124 43 1.385 .722 .049 1.544 1.64 4.205 80 354 4.654 .57 100 2730 9780 61 71 130 140 -50 654 561 93 1.29 564 4 .775 .087 .367 -3.521
8 2757 1140 151 324 2606 816 2265 871 187 360 2114 547 0 0 2267 715 241 312 91 70 81 46 3422 2661 3.194 .313 .259 .344 .316 2.124 80 455 .3 .9 110 2850 9750 57 68 141 152 0 2036 579 1457 .559 1555 977 1.788 .462 -.839 -1.114
9 437 560 210 403 227 157 421 602 236 431 211 199 0 0 180 218 116 199 66 50 50 16 384 410 1.446 .692 .943 .884 .895 2.948 12 80 2.253 .42 50 3020 9750 60 65 161 166 0 1000 720 280 1.235 1075 355 .81 1.684 .305 .752
10 670 683 192 371 478 312 686 733 190 386 494 362 0 0 88 214 76 184 100 66 100 50 790 856 1.532 .653 .733 .624 .916 1.947 12 80 13.436 .62 50 3170 9750 60 65 176 181 0 1220 663 557 1.166 1309 646 .858 1.309 .221 .388
11 295 517 165 344 130 173 209 449 179 365 44 105 0 0 241 239 88 157 41 41 27 23 303 149 .751 1.331 2.386 .97 1.13 4.339 80 352 1.152 .39 100 3360 9780 61 71 193 203 -50 923 614 309 2.376 802 188 .421 4.261 1.249 2.091
12 308 489 176 364 132 125 254 423 185 382 78 59 0 0 187 265 81 152 48 38 31 21 257 137 1.056 .947 .756 1.11 1.141 3.797 80 324 1.993 .4 100 3510 9780 61 71 208 218 -50 873 650 223 1.691 755 105 .591 1.351 .758 .434
13 303 558 170 370 133 188 228 479 182 391 58 109 0 0 233 271 90 169 42 38 27 23 321 167 .707 1.414 1.879 1.444 1.294 3.172 80 348 1.768 .47 100 3670 9780 61 71 224 234 -50 996 661 336 2.524 855 195 .396 3.356 1.336 1.747
14 1966 1801 172 385 1794 1416 1386 1418 185 394 1214 1033 0 0 1609 1283 87 160 97 88 88 80 3210 2247 1.267 .789 .851 .709 .845 2.458 80 371 .776 .89 100 3790 9750 58 68 236 246 0 3216 688 2529 1.409 2532 1845 .709 1.519 .495 .604
15 306 534 175 395 131 139 233 459 194 411 58 64 0 0 227 295 95 163 41 35 27 26 270 122 .942 1.061 1.103 1.429 1.672 3.651 80 369 1.642 .62 100 3980 9780 61 71 255 265 -50 954 705 248 1.895 820 114 .528 1.97 .922 .979
16 1898 4663 164 372 1734 4291 1301 3450 175 391 1137 3078 0 0 1524 3692 78 169 96 96 91 92 6025 4215 .404 2.475 2.707 2.363 2.438 1.703 80 372 2.567 .94 100 4110 9750 58 68 268 278 0 8327 664 7663 4.419 6161 5496 .226 4.834 2.144 2.273
17 249 444 162 351 87 93 192 399 177 371 30 48 0 0 163 209 90 159 33 31 21 15 180 78 .935 1.069 1.6 1.146 1.062 3.457 80 415 2.589 .38 100 4300 9780 61 71 287 297 -50 793 627 166 1.909 713 86 .524 2.857 .933 1.515
18 294 422 164 336 130 86 210 364 173 360 46 28 0 0 223 188 77 152 40 28 25 12 216 74 1.512 .662 .609 1.205 .99 4.606 80 310 1.331 .37 100 4450 9780 61 71 302 312 -50 754 600 154 1.181 650 50 .847 1.087 .24 .12
19 886 1113 173 353 713 760 851 1071 178 371 678 718 0 0 422 446 71 156 95 90 91 81 1473 1396 .938 1.066 1.059 1.034 1.002 2.085 80 357 1.111 .81 100 4580 9750 58 68 315 325 0 1988 630 1357 1.903 1913 1282 .525 1.891 .929 .919
20 222 395 174 356 48 39 164 367 185 561 -10 11 0 0 159 169 105 3255 23 0 15 0 87 1 1.231 .813 null 1.189 1.199 3.392 80 380 2.429 .27 100 4770 9780 61 71 334 344 -50 705 636 70 1.451 655 20 .689 null .537 null

Total number of rows: 37632

Table truncated, full table size 8360 Kbytes.




Supplementary data files not provided
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