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Sample GSM91720 Query DataSets for GSM91720
Status Public on Jan 11, 2006
Title "088 Day0 in-vivo SP Inf, PBMC 2nd 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 "088 Day0 in-vivo SP Inf, PBMC 2nd TC"
Organism Homo sapiens
Characteristics "088 Day0 in-vivo SP Inf, PBMC 2nd TC"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/19446.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 3295 3946 391 721 2904 3225 3212 4023 402 722 2821 3302 0 0 707 775 92 126 100 100 100 100 6129 6123 .9 1.111 1.171 1.112 1.146 1.234 80 412 1.127 .97 100 1820 9070 106 116 93 103 0 4995 913 4082 1.406 5092 4180 .711 1.482 .491 .567
2 2725 6017 404 739 2321 5278 2798 5971 429 761 2394 5232 0 0 471 1159 138 220 100 100 100 100 7599 7626 .44 2.274 2.185 2.271 2.267 1.237 52 311 2.382 .95 90 1960 9070 106 115 107 116 0 7616 935 6681 2.879 7558 6623 .347 2.766 1.525 1.468
3 4476 9487 405 700 4071 8787 4602 9635 425 733 4197 8935 0 0 1029 2118 125 221 100 100 100 100 12858 13132 .463 2.158 2.129 2.168 2.103 1.199 52 336 2.175 .98 90 2120 9060 105 114 123 132 0 12009 886 11123 2.732 12196 11310 .366 2.695 1.45 1.43
4 7566 5303 405 743 7161 4560 7384 5281 411 745 6979 4538 0 0 2162 1633 80 132 100 100 100 100 11721 11517 1.57 .637 .65 .614 .651 1.247 80 388 .649 .98 100 2290 9070 106 116 140 150 0 6713 941 5772 .806 6685 5744 1.241 .823 -.311 -.281
5 5520 9524 405 752 5115 8772 5742 9440 417 762 5337 8688 0 0 1671 2845 113 135 100 100 100 100 13887 14025 .583 1.715 1.628 1.71 1.72 1.212 52 312 1.724 .98 90 2430 9060 105 114 154 163 0 12056 952 11104 2.171 11949 10997 .461 2.061 1.118 1.043
6 46904 27892 421 755 46483 27137 47919 28059 457 779 47498 27304 3 0 11467 8135 297 164 100 100 100 100 73620 74802 1.713 .584 .575 .569 .586 1.219 80 409 .589 .99 100 2600 9070 106 116 171 181 0 35306 956 34351 .739 35518 34562 1.353 .728 -.436 -.459
7 1462 2064 418 788 1044 1276 667 865 425 790 249 77 0 0 1513 2259 90 124 83 45 60 38 2320 326 .818 1.222 .309 .778 1.26 3.293 80 345 1.446 .97 100 2760 9070 106 116 187 197 -50 2613 997 1615 1.547 1095 97 .646 .391 .63 -1.353
8 9368 8531 409 802 8959 7729 10048 8862 417 802 9639 8060 0 0 3043 3089 91 125 100 100 100 100 16688 17699 1.159 .863 .836 .819 .86 1.346 80 372 .88 .98 100 2900 9060 105 115 201 211 0 10799 1015 9784 1.092 11218 10203 .916 1.058 .127 .082
9 2307 7510 411 794 1896 6716 2303 7551 417 801 1892 6757 0 0 487 1420 78 126 100 100 100 100 8612 8649 .282 3.542 3.571 3.589 3.572 1.179 80 373 3.534 .97 100 3060 9070 106 116 217 227 0 9506 1005 8501 4.484 9558 8553 .223 4.521 2.165 2.177
10 8050 12883 495 827 7555 12056 7236 11857 503 836 6741 11030 0 0 4824 6014 125 128 98 100 96 100 19611 17771 .627 1.596 1.636 1.994 1.592 1.855 80 387 1.493 .97 100 3220 9070 106 116 233 243 0 16308 1047 15261 2.02 15009 13962 .495 2.071 1.014 1.05
11 3812 5467 568 854 3244 4613 3890 5383 585 854 3322 4529 0 0 1494 1822 107 127 100 100 98 100 7857 7851 .703 1.422 1.363 1.517 1.409 1.422 80 374 1.39 .98 100 3380 9070 106 116 249 259 0 6920 1081 5839 1.8 6814 5733 .556 1.726 .848 .787
12 4085 6174 555 847 3530 5327 4044 6046 569 864 3489 5199 0 0 1305 1943 108 181 100 100 100 100 8857 8688 .663 1.509 1.49 1.505 1.547 1.359 80 381 1.527 .96 100 3540 9060 105 115 265 275 0 7815 1072 6743 1.91 7653 6581 .524 1.886 .934 .915
13 4507 8723 504 865 4003 7858 4556 8667 516 878 4052 7802 0 0 1442 2723 112 188 100 100 100 100 11861 11854 .509 1.963 1.925 1.964 1.96 1.188 52 304 1.954 .97 90 3690 9060 105 114 280 289 0 11042 1095 9947 2.485 10971 9876 .402 2.437 1.313 1.285
14 15052 18853 506 863 14546 17990 15112 18293 519 861 14606 17430 0 0 7024 6050 109 127 100 100 100 100 32536 32036 .809 1.237 1.193 1.357 1.236 1.416 80 394 1.16 .97 100 3850 9060 105 115 296 306 0 23865 1092 22772 1.566 23156 22063 .639 1.511 .647 .595
15 5639 8230 513 888 5126 7342 5083 7687 521 905 4570 6799 0 0 2649 3003 108 238 96 100 96 100 12468 11369 .698 1.432 1.488 1.511 1.441 1.384 80 367 1.365 .98 100 4010 9070 106 116 312 322 0 10418 1124 9294 1.813 9730 8606 .552 1.883 .858 .913
16 9574 32346 448 852 9126 31494 9559 31952 458 886 9111 31100 0 0 3011 9352 108 242 100 100 100 100 40620 40211 .29 3.451 3.413 3.524 3.403 1.264 80 378 3.468 .98 100 4170 9070 106 116 328 338 0 40944 1078 39866 4.368 40446 39367 .229 4.321 2.127 2.111
17 4068 5666 415 803 3653 4863 3912 5404 418 814 3497 4601 0 0 1341 1671 80 137 100 100 100 100 8516 8098 .751 1.331 1.316 1.34 1.355 1.218 52 318 1.377 .96 90 4320 9060 105 114 343 352 0 7172 1016 6156 1.685 6841 5824 .593 1.665 .753 .736
18 1880 2642 401 768 1479 1874 2013 2686 409 776 1612 1918 0 0 632 899 83 126 96 100 96 100 3353 3530 .789 1.267 1.19 1.282 1.27 1.661 32 172 1.275 .95 60 4470 9070 108 114 360 366 0 3344 972 2372 1.604 3400 2428 .623 1.506 .682 .591
19 3359 14408 392 803 2967 13605 3369 14409 402 852 2977 13606 0 0 796 3224 101 296 100 100 100 100 16572 16583 .218 4.585 4.57 4.725 4.465 1.397 80 406 4.655 .96 100 4640 9070 106 116 375 385 0 18238 1016 17222 5.804 18239 17223 .172 5.785 2.537 2.532
20 1388 1725 384 821 1004 904 1469 1821 404 830 1085 1000 0 0 421 439 182 194 94 88 88 84 1908 2085 1.111 .9 .922 .831 .924 1.997 52 315 .928 .84 90 4790 9060 105 114 390 399 0 2184 1039 1144 1.14 2305 1266 .877 1.167 .189 .222

Total number of rows: 37632

Table truncated, full table size 8664 Kbytes.




Supplementary data files not provided

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