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Sample GSM91850 Query DataSets for GSM91850
Status Public on Jan 11, 2006
Title "099 Day10 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 Day10 in-vivo SP Inf, PBMC 1st TC, relabel"
Organism Homo sapiens
Characteristics "099 Day10 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/2001-08/19505.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 8647 10855 232 296 8415 10559 8879 11310 252 309 8647 11014 0 0 2508 3888 108 120 100 100 100 100 18974 19661 .797 1.255 1.274 1.209 1.263 1.403 80 488 1.299 .96 110 1400 9010 75 86 74 85 0 7189 196 6993 .831 7490 7294 1.203 .844 -.267 -.245
2 2316 8079 236 290 2080 7789 2440 8109 347 367 2204 7819 0 0 741 2368 1056 641 90 100 57 100 9869 10023 .267 3.745 3.548 3.996 3.748 1.494 80 418 3.414 .64 110 1570 9020 76 87 91 102 0 5350 192 5158 2.48 5370 5178 .403 2.349 1.31 1.232
3 9905 18833 226 280 9679 18553 10312 20257 227 300 10086 19977 0 0 2180 5550 62 109 100 100 100 100 28232 30063 .522 1.917 1.981 1.836 1.932 1.378 80 419 2.019 .96 110 1720 9010 75 86 106 117 0 12472 185 12287 1.269 13415 13230 .788 1.312 .344 .391
4 15594 6277 219 290 15375 5987 15877 6226 229 315 15658 5936 0 0 4773 2262 84 159 100 100 100 100 21362 21594 2.568 .389 .379 .378 .388 1.511 80 421 .38 .94 110 1880 9010 75 86 122 133 0 4157 192 3965 .258 4123 3931 3.878 .251 -1.955 -1.994
5 7558 10144 212 287 7346 9857 6717 10360 220 309 6505 10073 0 0 3831 5352 71 160 100 100 100 100 17203 16578 .745 1.342 1.549 1.249 1.354 1.826 80 366 1.393 .92 100 2030 9000 75 85 138 148 0 6718 190 6528 .889 6861 6671 1.125 1.025 -.17 .036
6 44433 20090 240 313 44193 19777 48604 21334 266 337 48364 21021 0 0 12061 4457 102 151 100 100 100 100 63970 69385 2.235 .448 .435 .46 .44 1.339 80 409 .42 .95 100 2190 9010 76 86 154 164 0 13305 207 13097 .296 14128 13921 3.374 .288 -1.755 -1.797
7 3158 6668 344 417 2814 6251 2445 5315 381 459 2101 4898 0 0 1961 4539 171 281 100 100 100 100 9065 6999 .45 2.221 2.331 2.169 2.306 1.48 32 212 2.574 .91 70 2350 9010 77 84 171 178 0 4416 276 4140 1.471 3520 3244 .68 1.544 .557 .627
8 13467 19818 250 325 13217 19493 14187 20706 298 377 13937 20381 0 0 4192 5061 189 245 100 100 100 100 32710 34318 .678 1.475 1.462 1.547 1.512 1.443 80 459 1.456 .96 110 2500 9010 75 86 184 195 0 13125 215 12909 .977 13713 13497 1.024 .968 -.034 -.046
9 2372 13185 204 294 2168 12891 2431 13318 226 307 2227 13024 0 0 701 3382 118 135 100 100 100 100 15059 15251 .168 5.946 5.848 6.123 5.863 1.377 80 381 6.106 .91 100 2660 9010 76 86 201 211 0 8732 195 8537 3.938 8820 8625 .254 3.873 1.977 1.953
10 7215 18468 207 293 7008 18175 6378 18149 215 304 6171 17856 0 0 4237 8381 84 114 100 100 100 100 25183 24027 .386 2.593 2.894 2.972 2.654 1.563 80 352 2.484 .95 100 2820 9020 77 87 217 227 0 12230 194 12036 1.718 12019 11825 .582 1.916 .78 .938
11 4122 9563 196 289 3926 9274 3969 8998 200 297 3773 8709 0 0 1868 3771 49 107 100 100 100 100 13200 12482 .423 2.362 2.308 2.477 2.37 1.348 80 403 2.324 .96 110 2970 9010 75 86 231 242 0 6333 191 6142 1.564 5959 5768 .639 1.529 .646 .612
12 6779 16542 198 298 6581 16244 6685 16779 203 307 6487 16481 0 0 1729 4240 54 105 100 100 100 100 22825 22968 .405 2.468 2.541 2.468 2.508 1.213 80 347 2.543 .97 100 3130 9010 76 86 248 258 0 10955 197 10758 1.635 11112 10915 .612 1.683 .709 .751
13 3295 11277 192 320 3103 10957 3147 10366 200 328 2955 10046 0 0 1213 4967 56 112 100 100 100 100 14060 13001 .283 3.531 3.4 3.452 3.613 1.322 80 347 3.738 .97 100 3280 9010 76 86 263 273 0 7468 212 7256 2.338 6865 6653 .428 2.251 1.226 1.171
14 15577 24746 183 314 15394 24432 16333 25657 188 320 16150 25343 0 0 4417 5745 46 105 100 100 100 100 39826 41493 .63 1.587 1.569 1.617 1.595 1.304 80 416 1.586 .96 110 3440 9010 75 86 278 289 0 16388 208 16180 1.051 16991 16783 .951 1.039 .072 .056
15 4798 11237 193 333 4605 10904 4518 10689 216 406 4325 10356 0 0 1953 4379 109 310 100 100 100 100 15509 14681 .422 2.368 2.394 2.372 2.371 1.29 80 364 2.395 .97 100 3590 9010 76 86 294 304 0 7442 221 7221 1.568 7079 6858 .638 1.586 .649 .665
16 10269 43108 201 342 10068 42766 10822 47085 232 434 10621 46743 0 3 4169 17817 123 344 100 100 100 100 52834 57364 .235 4.248 4.401 4.319 4.373 1.346 80 398 4.365 .97 110 3750 9020 76 87 309 320 0 28548 226 28322 2.813 31182 30956 .355 2.915 1.492 1.543
17 2866 7169 187 322 2679 6847 2805 6959 200 353 2618 6637 0 0 1158 2617 89 212 100 100 100 98 9526 9255 .391 2.556 2.535 2.615 2.646 1.46 80 367 2.591 .94 100 3890 9010 76 86 324 334 0 4748 213 4534 1.693 4609 4395 .591 1.679 .759 .748
18 2860 7298 190 343 2670 6955 2992 7458 196 351 2802 7115 0 0 854 2300 50 122 100 100 100 100 9625 9917 .384 2.605 2.539 2.613 2.691 1.375 80 377 2.682 .96 100 4060 9010 76 86 341 351 0 4833 227 4606 1.725 4939 4712 .58 1.682 .787 .75
19 3449 17398 190 321 3259 17077 3504 16985 206 388 3314 16664 0 0 821 3880 78 304 100 100 100 100 20336 19978 .191 5.24 5.028 5.292 5.221 1.228 80 412 5.283 .97 110 4210 9010 75 86 355 366 0 11522 213 11309 3.47 11248 11036 .288 3.33 1.795 1.736
20 1317 2324 194 346 1123 1978 1395 2504 263 447 1201 2158 0 0 350 681 182 340 98 98 95 95 3101 3359 .568 1.761 1.797 1.727 1.768 1.377 80 355 1.917 .91 100 4370 9010 76 86 372 382 0 1539 229 1310 1.166 1658 1429 .857 1.19 .222 .251

Total number of rows: 37632

Table truncated, full table size 8737 Kbytes.




Supplementary data files not provided
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