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Sample GSM91808 Query DataSets for GSM91808
Status Public on Jan 11, 2006
Title "083 Day0 in-vivo SP Inf, PBMC 3rd 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 "083 Day0 in-vivo SP Inf, PBMC 3rd TC, relabel"
Organism Homo sapiens
Characteristics "083 Day0 in-vivo SP Inf, PBMC 3rd TC, relabel"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21407.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 4494 2568 153 516 4341 2052 4595 2365 182 531 4442 1849 0 0 1022 942 96 125 100 100 100 98 6393 6291 2.115 .473 .416 .44 .433 1.372 80 511 .501 .93 110 1570 9110 49 60 39 50 0 3292 662 2631 .606 3032 2371 1.65 .534 -.723 -.906
2 1492 4299 184 539 1308 3760 1539 3999 251 579 1355 3460 0 0 410 1726 161 168 100 100 100 100 5068 4815 .348 2.875 2.554 2.705 2.863 1.284 80 413 3.247 .95 110 1730 9110 49 60 55 66 0 5512 691 4821 3.685 5127 4436 .271 3.274 1.882 1.711
3 7309 11504 183 535 7126 10969 7343 11261 256 572 7160 10726 0 0 1261 3405 171 168 100 100 100 100 18095 17886 .65 1.539 1.498 1.483 1.53 1.226 80 401 1.613 .97 110 1890 9120 50 61 71 82 0 14749 686 14063 1.973 14437 13751 .507 1.921 .981 .942
4 14317 5673 174 526 14143 5147 14716 5874 222 538 14542 5348 0 0 2309 1734 142 123 100 100 100 100 19290 19890 2.748 .364 .368 .347 .351 1.246 80 413 .372 .96 110 2040 9110 49 60 86 97 0 7273 674 6599 .467 7531 6856 2.143 .471 -1.1 -1.085
5 5469 6185 170 543 5299 5642 4976 4795 237 593 4806 4252 0 0 3090 4054 189 480 100 98 100 96 10941 9058 .939 1.065 .885 .97 1.019 1.363 80 370 1.175 .98 100 2190 9110 50 60 102 112 0 7929 696 7233 1.365 6147 5451 .733 1.134 .449 .182
6 33451 8179 182 577 33269 7602 32165 7748 323 627 31983 7171 0 0 8549 2896 333 446 100 100 100 100 40871 39154 4.376 .229 .224 .219 .218 1.267 80 476 .229 .97 110 2350 9100 48 59 117 128 0 10486 740 9746 .293 9933 9194 3.414 .287 -1.771 -1.799
7 4427 3775 738 759 3689 3016 4299 3284 880 776 3561 2525 0 0 1127 1973 512 283 100 100 100 100 6705 6086 1.223 .818 .709 .733 .708 1.521 12 104 .887 .89 50 2520 9100 51 56 137 142 -100 4840 973 3867 1.048 4210 3237 .954 .909 .068 -.138
8 8933 6969 334 708 8599 6261 8863 7201 521 746 8529 6493 0 0 1560 2077 486 234 100 100 100 100 14860 15022 1.373 .728 .761 .695 .713 1.264 80 461 .77 .97 110 2660 9100 48 59 148 159 -100 8935 908 8027 .933 9232 8324 1.071 .976 -.099 -.035
9 2235 8403 166 635 2069 7768 1551 5819 353 684 1385 5184 0 0 1522 6303 398 226 100 100 98 100 9837 6569 .266 3.754 3.743 3.486 3.539 1.381 80 447 4.268 .93 110 2810 9090 47 58 163 174 -100 10773 814 9959 4.813 7460 6646 .208 4.799 2.267 2.263
10 2465 4913 133 502 2332 4411 2088 4058 169 523 1955 3556 0 0 1396 2948 178 150 100 100 100 100 6743 5511 .529 1.892 1.819 1.835 1.869 1.321 80 383 2.003 .98 100 2970 9090 48 58 180 190 0 6299 644 5655 2.425 5203 4559 .412 2.332 1.278 1.222
11 1749 2760 144 475 1605 2285 1737 2654 162 486 1593 2179 0 0 690 1205 83 117 100 100 100 100 3890 3772 .702 1.424 1.368 1.342 1.373 1.339 80 338 1.553 .95 100 3130 9100 49 59 196 206 0 3538 609 2929 1.825 3403 2794 .548 1.754 .868 .81
12 1467 2579 161 521 1306 2058 1443 2541 174 519 1282 2020 0 0 384 766 74 115 100 100 100 100 3364 3302 .635 1.576 1.576 1.532 1.542 1.282 80 384 1.744 .94 100 3280 9100 49 59 211 221 0 3306 668 2638 2.02 3258 2590 .495 2.02 1.015 1.014
13 1934 3414 148 552 1786 2862 1606 2826 157 560 1458 2274 0 0 878 1999 61 147 100 100 100 100 4648 3732 .624 1.602 1.56 1.45 1.503 1.404 52 277 1.853 .96 80 3440 9090 49 57 228 236 0 4377 708 3669 2.054 3623 2915 .487 2 1.039 1
14 8199 10991 146 592 8053 10399 7871 10216 159 602 7725 9624 0 0 1892 3178 70 154 100 100 100 100 18452 17349 .774 1.291 1.246 1.269 1.249 1.139 80 405 1.335 .98 100 3600 9100 49 59 243 253 0 14091 759 13332 1.656 13097 12338 .604 1.597 .727 .676
15 1806 3547 147 606 1659 2941 1784 3307 153 614 1637 2701 0 0 662 1411 55 131 100 100 100 100 4600 4338 .564 1.773 1.65 1.735 1.734 1.299 80 443 1.888 .96 110 3750 9090 47 58 257 268 0 4547 777 3771 2.273 4240 3463 .44 2.115 1.184 1.081
16 6202 17136 158 634 6044 16502 6146 16260 181 662 5988 15626 0 0 1359 5088 105 196 100 100 100 100 22546 21614 .366 2.73 2.61 2.667 2.667 1.166 80 457 2.835 .98 110 3910 9090 47 58 273 284 0 21969 813 21156 3.5 20846 20033 .286 3.346 1.808 1.742
17 1182 2318 178 650 1004 1668 1103 2217 218 701 925 1567 0 0 467 903 128 233 100 100 98 93 2672 2492 .602 1.661 1.694 1.559 1.653 1.425 80 391 1.81 .95 100 4070 9100 49 59 290 300 0 2972 833 2138 2.13 2842 2009 .469 2.172 1.091 1.119
18 1225 2263 154 579 1071 1684 1239 2144 169 613 1085 1565 0 0 435 925 84 165 100 100 100 98 2755 2650 .636 1.572 1.442 1.475 1.521 1.476 52 339 1.761 .91 90 4220 9090 48 57 305 314 0 2901 742 2159 2.016 2749 2006 .496 1.849 1.011 .887
19 2362 10462 152 591 2210 9871 2143 9071 181 621 1991 8480 0 0 780 4041 108 178 100 100 100 100 12081 10471 .224 4.467 4.259 4.4 4.501 1.159 80 456 4.826 .97 110 4390 9100 48 59 321 332 0 13413 758 12655 5.726 11629 10872 .175 5.46 2.518 2.449
20 682 1218 233 680 449 538 701 1205 299 763 468 525 0 0 104 347 198 275 98 73 69 46 987 993 .835 1.198 1.122 1.084 1.165 2.052 52 326 1.781 .74 90 4540 9080 47 56 337 346 0 1562 872 690 1.536 1545 673 .651 1.438 .619 .524

Total number of rows: 37632

Table truncated, full table size 8479 Kbytes.




Supplementary data files not provided
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