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Sample GSM91844 Query DataSets for GSM91844
Status Public on Jan 11, 2006
Title "099 Day3 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 Day3 in-vivo SP Inf, PBMC 1st TC, relabel"
Organism Homo sapiens
Characteristics "099 Day3 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/2001-08/19501.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 7288 7825 174 410 7114 7415 7607 7907 199 431 7433 7497 0 0 2307 3018 100 155 100 100 100 100 14529 14930 .959 1.042 1.009 1.011 1.042 1.334 80 490 1.077 .96 110 1570 9440 102 113 75 86 0 6113 320 5793 .814 6177 5857 1.228 .788 -.296 -.344
2 1936 7006 176 416 1760 6590 1945 7043 213 463 1769 6627 0 0 592 2251 124 222 100 100 100 100 8350 8396 .267 3.744 3.746 3.728 3.711 1.262 80 400 3.951 .96 110 1720 9440 102 113 90 101 0 5473 325 5148 2.925 5502 5177 .342 2.927 1.549 1.549
3 5822 10485 162 372 5660 10113 6806 11323 174 409 6644 10951 0 0 3067 5366 76 197 100 98 98 97 15773 17595 .56 1.787 1.648 1.811 1.761 1.621 120 441 1.805 .97 120 1880 9450 103 115 106 118 0 8191 291 7901 1.396 8846 8555 .716 1.288 .481 .365
4 13937 5300 159 382 13778 4918 13495 5213 177 416 13336 4831 0 0 3298 1371 83 192 100 100 100 100 18696 18167 2.802 .357 .362 .354 .354 1.202 80 386 .352 .97 110 2040 9440 102 113 122 133 0 4141 298 3842 .279 4073 3774 3.586 .283 -1.842 -1.821
5 6432 8703 160 397 6272 8306 6110 8186 186 433 5950 7789 0 0 3057 4191 100 189 100 100 100 98 14578 13739 .755 1.324 1.309 1.273 1.303 1.341 80 428 1.343 .98 110 2190 9430 101 112 137 148 0 6799 310 6489 1.035 6395 6085 .967 1.023 .049 .032
6 53202 21949 169 396 53033 21553 58685 22558 183 416 58516 22162 17 0 13479 7410 78 148 100 100 100 100 74586 80678 2.461 .406 .379 .387 .401 1.305 80 462 .405 .97 110 2350 9430 101 112 153 164 0 17148 309 16838 .318 17623 17314 3.15 .296 -1.655 -1.757
7 2139 4425 182 405 1957 4020 1891 4159 195 411 1709 3754 0 0 1309 2791 73 133 100 98 100 98 5977 5463 .487 2.054 2.197 2.072 2.024 1.429 52 250 2.146 .97 80 2510 9440 104 112 171 179 0 3457 316 3141 1.605 3249 2933 .623 1.716 .682 .779
8 8949 12411 179 420 8770 11991 9277 12135 196 433 9098 11715 0 0 5343 7628 109 146 99 100 99 100 20761 20813 .731 1.367 1.288 1.363 1.374 1.474 120 493 1.396 .99 120 2670 9440 102 114 185 197 0 9696 328 9368 1.068 9480 9152 .936 1.006 .095 .009
9 1783 9471 179 428 1604 9043 1796 9391 198 451 1617 8963 0 0 523 2674 110 159 100 100 100 100 10647 10580 .177 5.638 5.543 5.764 5.564 1.275 80 395 5.742 .97 110 2820 9430 101 112 200 211 0 7399 334 7065 4.405 7337 7002 .227 4.33 2.139 2.115
10 3572 14066 189 423 3383 13643 3383 13706 197 434 3194 13283 0 0 1488 5801 69 135 100 100 100 100 17026 16477 .248 4.033 4.159 4.084 4.072 1.24 80 374 4.049 .98 100 2980 9440 103 113 217 227 0 10989 330 10659 3.151 10708 10377 .317 3.249 1.656 1.7
11 2605 5989 199 427 2406 5562 2578 5624 207 445 2379 5197 0 0 874 2055 80 138 100 100 100 100 7968 7576 .433 2.312 2.185 2.312 2.288 1.225 80 422 2.35 .98 110 3140 9430 101 112 232 243 0 4679 334 4345 1.806 4394 4060 .554 1.707 .853 .771
12 2339 8556 201 433 2138 8123 2204 8226 203 452 2003 7793 0 0 952 3180 50 143 100 100 100 100 10261 9796 .263 3.799 3.891 3.925 3.879 1.253 80 353 3.762 .98 100 3290 9430 102 112 248 258 0 6684 338 6346 2.968 6427 6088 .337 3.04 1.57 1.604
13 2783 10422 197 444 2586 9978 2703 10156 203 463 2506 9712 0 0 963 4624 60 154 100 100 100 100 12564 12218 .259 3.858 3.875 3.714 3.701 1.266 52 322 4.057 .98 90 3440 9430 102 111 263 272 0 8142 347 7795 3.014 7934 7588 .332 3.028 1.592 1.598
14 8657 20214 191 443 8466 19771 8837 19890 197 460 8646 19447 0 0 2415 5594 53 150 100 100 100 100 28237 28093 .428 2.335 2.249 2.353 2.305 1.195 80 481 2.359 .98 110 3610 9430 101 112 279 290 0 15792 346 15446 1.824 15539 15193 .548 1.757 .867 .813
15 3469 10446 191 453 3278 9993 3315 10326 208 477 3124 9873 0 0 1383 3998 119 204 100 100 100 100 13271 12997 .328 3.049 3.16 3.137 3.029 1.262 80 365 3.044 .99 110 3770 9440 102 113 295 306 0 8161 354 7807 2.382 8067 7713 .42 2.469 1.252 1.304
16 5875 16806 189 469 5686 16337 5291 12442 205 494 5102 11973 0 0 4895 15202 103 200 98 100 98 98 22023 17075 .348 2.873 2.347 2.568 2.636 1.596 156 725 3.04 .98 150 3920 9420 98 113 308 323 0 13130 366 12763 2.245 9720 9354 .445 1.833 1.167 .875
17 2026 5486 194 456 1832 5030 1963 5258 203 467 1769 4802 0 0 750 2123 75 145 100 100 100 100 6862 6571 .364 2.746 2.715 2.72 2.758 1.201 80 355 2.814 .98 100 4080 9430 102 112 327 337 0 4286 356 3930 2.145 4108 3752 .466 2.121 1.101 1.085
18 1762 3803 211 401 1551 3402 1863 3878 221 415 1652 3477 0 0 419 891 60 119 100 100 100 100 4953 5129 .456 2.193 2.105 2.218 2.174 1.198 32 197 2.255 .98 70 4230 9420 102 109 343 350 0 2971 313 2658 1.714 3030 2716 .584 1.644 .777 .717
19 1971 9062 204 420 1767 8642 2111 10623 216 445 1907 10203 0 0 1181 5597 84 146 100 100 99 100 10409 12110 .204 4.891 5.35 5.053 4.833 1.365 156 659 4.903 .98 140 4390 9430 100 114 356 370 0 7080 328 6752 3.821 8299 7971 .262 4.18 1.934 2.063
20 827 1454 216 459 611 995 952 1527 277 506 736 1068 0 0 403 722 225 227 75 80 66 73 1606 1804 .614 1.628 1.451 1.802 1.699 1.776 120 451 1.759 .88 130 4550 9440 101 114 372 385 0 1136 359 777 1.272 1193 834 .786 1.134 .347 .181

Total number of rows: 37632

Table truncated, full table size 8635 Kbytes.




Supplementary data files not provided

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