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Sample GSM91824 Query DataSets for GSM91824
Status Public on Jan 11, 2006
Title "083 Day0 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 "083 Day0 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "083 Day0 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/2001-10/21411.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 1580 1288 215 663 1365 625 1157 1056 230 683 942 393 0 0 1097 578 98 186 98 76 98 52 1990 1335 2.184 .458 .417 .426 .464 1.978 80 421 .462 .89 100 1890 9710 56 66 51 61 0 831 428 403 .295 681 254 3.385 .269 -1.759 -1.893
2 576 1594 224 667 352 927 578 1621 286 779 354 954 0 0 176 414 304 528 59 84 6 25 1279 1308 .38 2.634 2.695 2.789 2.561 1.872 32 230 2.952 .76 70 2060 9690 55 62 69 76 0 1028 430 598 1.699 1046 615 .589 1.739 .765 .798
3 2163 4247 209 634 1954 3613 2089 4041 261 718 1880 3407 0 0 772 1523 293 478 100 100 96 96 5567 5287 .541 1.849 1.812 1.819 1.875 1.292 52 352 1.79 .96 90 2220 9690 54 63 84 93 0 2740 409 2331 1.193 2607 2198 .838 1.169 .254 .226
4 3454 1917 209 631 3245 1286 3373 1990 221 652 3164 1359 0 0 2009 857 102 157 100 90 98 83 4531 4523 2.523 .396 .43 .37 .391 1.537 80 412 .388 .95 100 2360 9700 55 65 98 108 0 1237 407 830 .256 1284 877 3.911 .277 -1.968 -1.851
5 846 1517 266 679 580 838 873 1514 316 715 607 835 0 0 283 519 152 218 91 83 83 75 1418 1442 .692 1.445 1.376 .978 1.224 2.838 12 104 1.469 .77 50 2520 9700 57 62 116 121 0 979 438 541 .932 977 539 1.073 .887 -.101 -.172
6 6866 2335 196 633 6670 1702 6170 2135 226 646 5974 1502 0 0 3928 1071 126 151 100 97 100 93 8372 7476 3.919 .255 .251 .242 .26 1.436 80 585 .252 .95 110 2670 9700 54 65 128 139 0 1506 408 1098 .165 1377 969 6.074 .162 -2.603 -2.624
7 796 2322 201 616 595 1706 807 2123 212 629 606 1507 0 0 157 1294 80 127 100 100 100 100 2301 2113 .349 2.867 2.487 2.45 1.96 2.121 12 98 5.009 .62 50 2840 9680 55 60 148 153 0 1498 397 1101 1.85 1370 972 .541 1.604 .887 .682
8 3144 2338 187 602 2957 1736 2610 2018 220 620 2423 1416 0 0 2597 1624 274 192 97 82 81 71 4693 3839 1.703 .587 .584 .512 .557 1.921 80 471 .571 .94 110 2980 9690 53 64 159 170 0 1508 388 1120 .379 1302 914 2.64 .377 -1.401 -1.407
9 384 1626 174 524 210 1102 329 1332 227 613 155 808 0 0 201 882 346 320 19 86 3 63 1312 963 .191 5.248 5.213 4.871 5.104 2.944 52 293 4.82 .5 90 3130 9710 56 65 175 184 0 1049 338 711 3.386 859 521 .295 3.363 1.759 1.75
10 388 1292 180 570 208 722 358 1093 191 607 178 523 0 0 181 618 92 225 70 83 48 52 930 701 .288 3.471 2.938 3.34 3.026 2.391 80 454 3.942 .78 110 3310 9710 55 66 192 203 0 834 368 466 2.239 705 337 .447 1.896 1.163 .923
11 716 1358 180 586 536 772 596 1266 237 608 416 680 0 0 382 657 284 176 69 78 42 63 1308 1096 .694 1.44 1.635 1.319 1.464 2.072 52 270 1.647 .87 80 3460 9710 57 65 209 217 0 876 378 498 .929 817 439 1.076 1.055 -.106 .077
12 312 1003 178 566 134 437 295 991 200 587 117 425 0 0 116 300 115 163 51 86 23 61 571 542 .307 3.261 3.632 3.365 3.391 2.421 80 490 3.497 .6 110 3630 9690 53 64 224 235 0 647 365 282 2.104 639 274 .475 2.344 1.073 1.229
13 301 670 182 559 119 111 279 641 203 606 97 82 0 0 140 215 111 340 42 7 20 3 230 179 1.072 .933 .845 1.248 1.306 2.794 80 379 1.737 .59 100 3810 9690 54 64 243 253 -50 432 361 72 .602 414 53 1.662 .545 -.733 -.875
14 2067 3294 184 518 1883 2776 1746 3015 192 551 1562 2497 0 0 1267 1878 80 335 100 98 100 91 4659 4059 .678 1.474 1.599 1.441 1.507 1.396 80 392 1.537 .94 110 3930 9690 53 64 254 265 0 2125 334 1791 .951 1945 1611 1.051 1.031 -.072 .045
15 464 1407 176 443 288 964 426 1208 186 462 250 765 0 0 206 699 69 116 88 96 71 88 1252 1015 .299 3.347 3.06 3.096 3.267 2.245 52 266 3.607 .81 80 4080 9690 55 63 271 279 0 908 286 622 2.159 779 494 .463 1.974 1.111 .981
16 1555 3915 177 446 1378 3469 1435 3594 184 460 1258 3148 0 0 967 2445 69 120 98 100 98 100 4847 4406 .397 2.517 2.502 2.6 2.58 1.574 80 486 2.623 .95 110 4240 9690 53 64 285 296 0 2526 288 2238 1.624 2319 2031 .616 1.614 .7 .691
17 229 651 181 491 48 160 205 598 195 504 24 107 0 0 96 229 96 132 28 46 10 26 208 131 .3 3.333 4.458 2.567 2.352 3.695 80 434 4.871 .35 100 4430 9690 54 64 305 315 -50 420 317 103 2.151 386 69 .465 2.876 1.105 1.524
18 317 712 173 509 144 203 236 685 184 514 63 176 0 0 202 242 76 127 45 55 35 36 347 239 .709 1.41 2.794 1.772 1.867 3.425 80 309 1.649 .6 100 4590 9690 54 64 321 331 -50 459 328 131 .909 442 114 1.1 1.802 -.137 .85
19 904 4611 174 539 730 4072 707 3035 183 551 533 2496 0 0 568 3068 72 141 91 100 87 100 4802 3029 .179 5.578 4.683 6.11 5.377 1.834 80 387 5.961 .95 110 4710 9690 53 64 332 343 0 2975 348 2627 3.599 1958 1610 .278 3.021 1.848 1.595
20 267 687 181 544 86 143 244 627 185 556 63 83 0 0 120 241 71 139 46 42 28 23 229 146 .601 1.663 1.317 1.731 1.83 3.884 80 378 3.299 .48 100 4900 9680 53 63 352 362 -50 443 351 92 1.073 405 54 .932 .85 .101 -.235

Total number of rows: 37632

Table truncated, full table size 8591 Kbytes.




Supplementary data files not provided
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