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Sample GSM91712 Query DataSets for GSM91712
Status Public on Jan 11, 2006
Title "282 Day14 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 Day14 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "282 Day14 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/2001-10/21505.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 1275 1008 103 447 1172 561 1096 1108 132 492 993 661 0 0 760 371 145 243 96 73 90 63 1733 1654 2.089 .479 .666 .481 .468 1.995 52 302 .486 .73 90 1730 9530 36 45 30 39 0 1200 532 668 .57 1319 787 1.755 .792 -.811 -.336
2 166 514 110 466 56 48 128 523 155 514 18 57 0 0 114 225 165 259 18 13 2 3 104 75 1.167 .857 3.167 3.167 2.684 4.072 80 435 2.191 .49 100 1930 9560 39 49 50 60 -50 612 555 57 1.02 623 68 .98 3.77 .029 1.915
3 1933 2049 111 513 1822 1536 2043 2058 213 554 1932 1545 0 0 821 926 255 294 100 87 90 75 3358 3477 1.186 .843 .8 .745 .768 1.523 32 169 .934 .9 70 2070 9530 37 44 65 72 0 2439 611 1829 1.004 2450 1839 .996 .952 .005 -.071
4 2212 1140 101 429 2111 711 2136 1108 116 463 2035 679 0 0 1203 566 99 218 100 76 100 63 2822 2714 2.969 .337 .334 .298 .352 1.923 80 414 .363 .84 100 2210 9530 36 46 78 88 0 1357 511 846 .401 1319 808 2.494 .397 -1.318 -1.332
5 347 666 106 425 241 241 202 571 122 458 96 146 0 0 339 404 72 217 55 45 46 32 482 242 1 1 1.521 1.316 1.367 3.985 80 367 1.688 .6 100 2400 9560 39 49 97 107 -50 793 506 287 1.19 680 174 .84 1.811 .252 .856
6 5702 1792 98 429 5604 1363 4545 1494 112 459 4447 1065 0 0 3969 1133 64 211 100 87 100 75 6967 5512 4.112 .243 .239 .223 .234 1.794 80 363 .252 .93 100 2520 9530 36 46 109 119 0 2133 511 1623 .29 1779 1268 3.454 .285 -1.788 -1.81
7 164 592 100 450 64 142 128 585 116 481 28 135 0 0 120 275 78 221 28 36 16 11 206 163 .451 2.219 4.821 3.394 3.549 3.652 80 397 10.315 .27 100 2710 9560 39 49 128 138 -50 705 536 169 2.641 696 161 .379 5.74 1.401 2.521
8 1522 1765 100 449 1422 1316 1137 1456 109 492 1037 1007 0 0 1210 1102 47 232 95 90 95 75 2738 2044 1.081 .925 .971 1.04 1.007 1.981 80 456 .949 .9 110 2850 9540 36 47 141 152 0 2101 535 1567 1.102 1733 1199 .908 1.156 .14 .209
9 296 750 115 481 181 269 274 732 125 571 159 251 0 0 128 323 62 303 81 37 62 12 450 410 .673 1.486 1.579 1.816 1.623 2.673 32 122 6.197 .33 60 3010 9520 37 43 160 166 0 893 573 320 1.769 871 299 .565 1.879 .823 .91
10 503 930 114 482 389 448 447 931 127 516 333 449 0 0 192 267 69 214 100 83 100 58 837 782 .868 1.152 1.348 1.484 1.606 1.579 12 90 2.543 .6 50 3180 9540 39 44 177 182 0 1107 574 533 1.371 1108 535 .729 1.605 .455 .683
11 232 566 101 454 131 112 169 510 109 477 68 56 0 0 167 286 46 212 56 26 42 12 243 124 1.17 .855 .824 1.844 1.847 4.738 80 425 3.851 .41 100 3340 9560 39 49 191 201 -50 674 540 133 1.018 607 67 .983 .98 .025 -.029
12 522 910 110 426 412 484 481 962 120 426 371 536 0 0 114 337 51 153 100 83 100 58 896 907 .851 1.175 1.445 .857 1.232 2.476 12 80 2.616 .63 50 3490 9530 38 43 208 213 0 1083 507 576 1.399 1145 638 .715 1.72 .484 .782
13 211 559 104 429 107 130 138 465 110 477 34 36 0 0 158 319 51 292 43 25 32 13 237 70 .823 1.215 1.059 2.131 2.167 3.339 80 374 4.86 .41 100 3660 9560 39 49 223 233 -50 665 511 155 1.446 554 43 .691 1.261 .532 .334
14 1092 2231 105 429 987 1802 690 1402 168 766 585 973 0 0 1012 1868 713 3442 40 20 23 1 2789 1558 .548 1.826 1.663 1.853 1.914 2.013 120 489 1.897 .96 120 3790 9540 36 48 235 247 -100 2656 511 2145 2.173 1669 1158 .46 1.98 1.12 .986
15 209 641 102 436 107 205 168 612 186 866 66 176 0 0 141 258 824 3975 0 0 0 0 312 242 .522 1.916 2.667 2.712 2.204 3.297 80 365 7.274 .34 100 3970 9560 39 49 254 264 -50 763 519 244 2.281 729 210 .438 3.175 1.19 1.667
16 1285 4167 105 412 1180 3755 925 2922 108 444 820 2510 0 0 967 3369 58 242 96 97 95 88 4935 3330 .314 3.182 3.061 2.935 3.142 1.885 80 370 3.398 .97 100 4110 9530 36 46 268 278 -100 4961 490 4470 3.788 3479 2988 .264 3.644 1.922 1.866
17 176 568 102 415 74 153 140 513 112 447 38 98 0 0 116 261 67 214 36 33 25 15 227 136 .484 2.068 2.579 2.075 3.041 4.465 80 415 10.603 .27 100 4280 9560 39 49 285 295 -50 676 494 182 2.461 611 117 .406 3.07 1.299 1.618
18 191 479 96 409 95 70 139 438 107 449 43 29 0 0 147 246 62 243 37 22 28 5 165 72 1.357 .737 .674 1.724 1.506 5.053 80 365 8.686 .24 100 4440 9560 39 49 301 311 -50 570 487 83 .877 521 35 1.14 .803 -.189 -.317
19 657 1592 98 413 559 1179 642 1643 107 443 544 1230 0 0 283 671 55 261 96 94 92 75 1738 1774 .474 2.109 2.261 2.168 1.93 1.759 52 311 2.604 .79 90 4580 9550 38 47 315 324 0 1895 492 1404 2.511 1956 1464 .398 2.692 1.328 1.429
20 178 531 97 429 81 102 140 494 103 464 43 65 0 0 120 272 50 263 45 18 30 7 183 108 .794 1.259 1.512 2.183 1.807 3.174 80 399 6.692 .46 100 4760 9560 39 49 333 343 -50 632 511 121 1.499 588 77 .667 1.8 .584 .848

Total number of rows: 37632

Table truncated, full table size 8400 Kbytes.




Supplementary data files not provided
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