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Sample GSM91704 Query DataSets for GSM91704
Status Public on Jan 11, 2006
Title "099 Day42 in-vivo SP Inf, PBMC 1st TC, relabel"
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 "099 Day42 in-vivo SP Inf, PBMC 1st TC, relabel"
Organism Homo sapiens
Characteristics "099 Day42 in-vivo SP Inf, PBMC 1st TC, relabel"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19511.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 GPL3346
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 5332 5418 306 551 5026 4867 5566 5229 312 549 5260 4678 0 0 1921 2184 71 140 100 100 100 100 9893 9938 1.033 .968 .889 .962 .952 1.304 80 377 1.001 .97 100 1470 9240 91 101 66 76 0 4925 501 4425 .88 4754 4253 1.136 .809 -.184 -.307
2 885 2216 299 533 586 1683 870 2193 304 543 571 1660 0 0 159 489 73 136 100 100 100 100 2269 2231 .348 2.872 2.907 2.85 2.968 1.31 80 401 3.14 .91 100 1630 9230 90 100 82 92 0 2015 485 1530 2.611 1994 1509 .383 2.643 1.385 1.402
3 5617 10144 307 542 5310 9602 5707 10408 321 555 5400 9866 0 0 1157 2615 94 151 100 100 100 100 14912 15266 .553 1.808 1.827 1.768 1.862 1.276 80 374 1.866 .97 100 1790 9230 90 100 98 108 0 9222 493 8729 1.644 9462 8969 .608 1.661 .717 .732
4 8305 3660 311 533 7994 3127 8436 3666 325 545 8125 3133 0 0 4753 1887 87 146 100 100 100 98 11121 11258 2.556 .391 .386 .4 .404 1.659 80 371 .382 .96 100 1940 9230 90 100 113 123 0 3327 485 2843 .356 3333 2848 2.812 .351 -1.492 -1.512
5 4747 8246 320 527 4427 7719 4801 7909 325 548 4481 7382 0 0 2310 3975 74 145 100 100 100 100 12146 11863 .574 1.744 1.647 1.798 1.804 1.378 80 400 1.759 .97 100 2100 9230 90 100 129 139 0 7496 479 7017 1.585 7190 6711 .631 1.498 .665 .583
6 24088 13077 303 524 23785 12553 24124 13260 313 541 23821 12736 0 0 5170 3451 76 147 100 100 100 100 36338 36557 1.895 .528 .535 .515 .527 1.274 80 480 .532 .97 110 2260 9230 89 100 144 155 0 11888 476 11412 .48 12055 11578 2.084 .486 -1.06 -1.041
7 1404 3101 309 522 1095 2579 1104 3249 320 537 795 2727 0 0 887 2096 75 119 93 96 93 87 3674 3522 .425 2.355 3.43 2.055 2.157 1.767 32 165 2.49 .93 60 2410 9220 91 97 162 168 0 2819 475 2345 2.141 2954 2479 .467 3.118 1.098 1.641
8 9867 8620 306 523 9561 8097 10620 9073 314 536 10314 8550 0 0 2768 3111 77 132 100 100 100 98 17658 18864 1.181 .847 .829 .766 .863 1.53 80 433 .881 .98 100 2580 9220 89 99 177 187 0 7836 475 7361 .77 8248 7773 1.299 .754 -.377 -.408
9 1207 8021 287 515 920 7506 1281 8473 293 528 994 7958 0 0 362 2538 73 139 98 100 97 100 8426 8952 .123 8.159 8.006 8.458 8.397 1.368 80 401 8.294 .95 100 2730 9230 90 100 192 202 0 7292 468 6824 7.417 7703 7235 .135 7.278 2.891 2.864
10 1721 8363 295 526 1426 7837 1644 7972 303 539 1349 7446 0 0 635 3491 68 143 100 100 100 100 9263 8795 .182 5.496 5.52 5.623 5.768 1.336 52 263 5.782 .96 80 2900 9240 92 100 210 218 0 7603 478 7125 4.996 7247 6769 .2 5.018 2.321 2.327
11 1905 4982 312 528 1593 4454 1842 4795 318 559 1530 4267 0 0 530 1543 76 175 100 100 100 100 6047 5797 .358 2.796 2.789 2.781 2.76 1.276 80 441 2.89 .96 100 3050 9230 90 100 224 234 0 4529 480 4049 2.542 4359 3879 .393 2.535 1.346 1.342
12 1361 5278 299 489 1062 4789 1476 5908 316 555 1177 5419 0 0 434 1679 85 238 100 100 96 100 5851 6596 .222 4.509 4.604 4.689 4.808 1.344 32 221 4.566 .92 70 3220 9220 90 97 242 249 0 4798 445 4354 4.099 5371 4926 .244 4.186 2.035 2.065
13 1963 9333 290 492 1673 8841 1972 9671 299 527 1682 9179 0 0 693 4119 80 186 100 100 100 100 10514 10861 .189 5.285 5.457 5.182 5.34 1.283 32 226 5.452 .96 70 3360 9220 90 97 256 263 0 8485 447 8037 4.804 8792 8345 .208 4.961 2.264 2.311
14 5976 13096 283 485 5693 12611 6258 13451 292 504 5975 12966 0 0 1337 3641 74 158 100 100 100 100 18304 18941 .451 2.215 2.17 2.143 2.205 1.332 80 417 2.309 .97 100 3530 9220 89 99 272 282 0 11905 441 11465 2.014 12228 11787 .497 1.973 1.01 .98
15 1999 7435 276 483 1723 6952 1892 7032 280 498 1616 6549 0 0 721 2787 65 139 98 100 98 100 8675 8165 .248 4.035 4.053 4.139 3.969 1.302 80 375 4.074 .97 100 3680 9230 90 100 287 297 0 6759 439 6320 3.668 6393 5954 .273 3.684 1.875 1.881
16 7742 28664 275 475 7467 28189 7686 28955 315 600 7411 28480 0 0 2667 10572 183 494 100 100 100 100 35656 35891 .265 3.775 3.843 3.769 3.83 1.211 80 440 3.847 .99 110 3840 9230 89 100 302 313 0 26058 432 25626 3.432 26323 25891 .291 3.494 1.779 1.805
17 842 1782 261 473 581 1309 843 1776 302 582 582 1303 0 0 176 390 189 490 100 98 85 82 1890 1885 .444 2.253 2.239 2.256 2.279 1.394 80 393 2.628 .89 100 4000 9230 90 100 319 329 0 1620 430 1190 2.048 1615 1185 .488 2.035 1.034 1.025
18 1037 1743 261 485 776 1258 1125 1787 267 510 864 1302 0 0 348 634 73 171 93 93 90 90 2034 2166 .617 1.621 1.507 1.659 1.525 1.653 32 159 1.807 .9 60 4150 9230 92 98 336 342 0 1585 441 1144 1.474 1625 1184 .679 1.37 .559 .454
19 1957 9691 261 475 1696 9216 2014 9986 272 537 1753 9511 0 0 588 2167 80 305 100 100 100 100 10912 11264 .184 5.434 5.426 5.775 5.285 1.37 80 453 5.275 .96 110 4300 9220 88 99 348 359 0 8810 432 8378 4.94 9078 8646 .202 4.932 2.305 2.302
20 925 1246 271 472 654 774 960 1240 284 496 689 768 0 0 261 297 88 198 97 96 92 92 1428 1457 .845 1.183 1.115 1.209 1.187 1.747 80 358 1.22 .87 100 4460 9220 89 99 365 375 0 1133 429 704 1.076 1127 698 .929 1.013 .106 .019

Total number of rows: 37632

Table truncated, full table size 8568 Kbytes.




Supplementary data files not provided

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