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Sample GSM91814 Query DataSets for GSM91814
Status Public on Jan 11, 2006
Title "282 Day -4 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
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 Day -4 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
Organism Homo sapiens
Characteristics "282 Day -4 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21483.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
1 406 425 91 239 315 186 114 258 221 312 23 19 0 0 760 539 437 303 16 17 11 12 501 42 1.694 .59 .826 1.647 1.818 3.746 80 422 .505 .84 100 1850 9910 50 60 57 67 -100 746 419 326 1.036 453 33 .965 1.449 .051 .535
2 390 814 119 288 271 526 163 349 227 358 44 61 0 0 1453 2819 373 327 10 13 3 6 797 105 .515 1.941 1.386 1.728 1.445 3.531 80 372 2.02 .91 100 2000 9910 50 60 72 82 -100 1428 505 923 3.405 612 107 .294 2.432 1.768 1.282
3 726 767 150 315 576 452 228 383 389 436 78 68 0 0 881 733 708 529 32 32 18 16 1028 146 1.274 .785 .872 .96 .965 3.009 80 386 2.026 .92 100 2160 9910 50 60 88 98 -100 1346 553 793 1.377 672 119 .726 1.529 .461 .613
4 954 540 151 293 803 247 176 317 357 387 25 24 0 0 1589 520 689 488 28 20 21 10 1050 49 3.251 .308 .96 .768 .595 4.395 80 341 .341 .64 100 2320 9910 50 60 104 114 -100 947 514 433 .54 556 42 1.853 1.684 -.89 .752
5 315 411 129 252 186 159 224 339 148 282 95 87 0 0 333 269 96 118 48 42 32 23 345 182 1.17 .855 .916 1.209 1.238 4.029 80 248 .694 .71 100 2470 9910 50 60 119 129 -50 721 442 279 1.5 595 153 .667 1.607 .585 .684
6 6794 2314 129 255 6665 2059 6207 2021 147 275 6078 1766 0 0 3986 1129 102 115 100 100 100 100 8724 7844 3.237 .309 .291 .318 .305 1.662 80 351 .274 .91 100 2580 9880 47 57 130 140 0 4060 447 3612 .542 3546 3098 1.845 .51 -.884 -.972
7 268 673 122 266 146 407 131 277 141 285 9 11 0 0 793 2928 91 125 27 23 12 11 553 20 .359 2.788 1.222 1.066 .959 3.504 80 384 3.801 .94 100 2780 9910 50 60 150 160 -50 1181 467 714 4.891 486 19 .204 2.144 2.29 1.1
8 2025 1234 123 300 1902 934 1734 949 151 350 1611 649 0 0 1602 875 108 233 100 70 95 58 2836 2260 2.036 .491 .403 .45 .485 2.353 80 441 .475 .85 110 2900 9880 46 57 161 172 0 2165 526 1639 .862 1665 1139 1.161 .707 -.215 -.501
9 280 510 135 319 145 191 219 433 195 407 84 114 0 0 203 315 353 503 17 13 0 1 336 198 .759 1.317 1.357 1.395 1.415 2.467 80 382 3.253 .87 100 3100 9910 50 60 182 192 -50 895 560 335 2.311 760 200 .433 2.381 1.208 1.252
10 893 1121 184 351 709 770 907 1089 195 391 723 738 0 0 261 214 124 189 100 100 91 100 1479 1461 .921 1.086 1.021 1.154 1.063 1.558 12 60 1.192 .8 50 3210 9870 48 53 195 200 0 1967 616 1351 1.905 1911 1295 .525 1.791 .93 .841
11 698 634 123 292 575 342 668 593 144 304 545 301 0 0 339 208 100 117 93 84 84 68 917 846 1.681 .595 .552 .621 .539 2.997 32 148 .564 .55 60 3370 9880 49 55 211 217 0 1112 512 600 1.043 1040 528 .958 .969 .061 -.046
12 728 868 176 302 552 566 741 841 195 311 565 539 0 0 176 373 122 122 100 91 91 83 1118 1104 .975 1.025 .954 1.012 1.056 1.799 12 72 1.372 .66 50 3530 9870 48 53 227 232 0 1523 530 993 1.799 1475 946 .556 1.674 .847 .743
13 208 333 116 265 92 68 167 293 139 278 51 28 0 0 144 163 100 116 36 32 18 18 160 79 1.353 .739 .549 1.34 1.149 3.417 80 373 .906 .62 100 3720 9910 50 60 244 254 -50 584 465 119 1.297 514 49 .771 .963 .375 -.054
14 1620 2167 120 285 1500 1882 1405 1928 140 298 1285 1643 0 0 1205 1500 91 133 95 95 93 90 3382 2928 .797 1.255 1.279 1.261 1.242 2.125 120 537 1.278 .91 120 3840 9880 46 58 255 267 0 3802 500 3302 2.201 3382 2882 .454 2.243 1.138 1.166
15 288 464 136 287 152 177 187 360 152 316 51 73 0 0 280 314 96 162 43 38 22 23 329 124 .859 1.164 1.431 1.725 1.481 3.203 80 353 1.011 .72 100 4040 9900 49 59 276 286 -50 814 504 311 2.043 632 128 .489 2.511 1.031 1.328
16 1867 3556 125 255 1742 3301 1369 2824 138 287 1244 2569 0 0 1465 2697 78 165 97 95 94 93 5043 3813 .528 1.895 2.065 1.869 1.863 1.985 120 498 1.92 .94 120 4150 9880 46 58 286 298 0 6239 447 5791 3.324 4954 4507 .301 3.623 1.733 1.857
17 207 420 124 257 83 163 154 354 137 279 30 97 0 0 157 277 73 164 40 36 21 15 246 127 .509 1.964 3.233 1.8 1.513 4.37 80 355 3.942 .39 100 4350 9900 49 59 307 317 -50 737 451 286 3.445 621 170 .29 5.673 1.785 2.504
18 272 333 131 269 141 64 227 312 161 300 96 43 0 0 210 174 269 217 16 23 5 2 205 139 2.203 .454 .448 1.228 1.215 3.139 80 314 .686 .77 100 4500 9900 49 59 322 332 -50 584 472 112 .796 547 75 1.256 .786 -.329 -.348
19 871 1733 128 279 743 1454 647 1329 225 380 519 1050 0 0 954 2644 646 687 45 65 11 40 2197 1569 .511 1.957 2.023 1.765 1.729 1.942 80 432 2.67 .93 110 4610 9900 48 59 332 343 -100 3040 489 2551 3.433 2332 1842 .291 3.549 1.78 1.828
20 407 915 120 252 287 663 194 295 218 353 74 43 0 0 951 4257 694 767 7 7 5 6 950 117 .433 2.31 .581 .82 .886 4.112 80 355 5.713 .37 100 4820 9900 49 59 354 364 -50 1605 442 1163 4.053 518 75 .247 1.019 2.019 .028

Total number of rows: 37632

Table truncated, full table size 8481 Kbytes.




Supplementary data files not provided
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