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Sample GSM71838 Query DataSets for GSM71838
Status Public on Aug 25, 2005
Title AD98 hpi 2
Sample type RNA
 
Channel 1
Source name Mock
Organism Homo sapiens
Characteristics Mock
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name AD169 98 hpi
Organism Homo sapiens
Characteristics AD169 98 hpi
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32567.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 Aug 24, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2779
Series (1)
GSE3194 Host cell gene expression late during cytomegalovirus infection

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
1 836 1907 213 779 623 1128 604 1478 215 814 391 699 0 0 770 1801 33 227 90 66 79 57 1751 1090 .552 1.811 1.788 1 1 1 120 502 1 .93 130 1730 8750 28 41 18 31 0 3126 1277 1849 2.968 2423 1146 .337 2.931 1.57 1.551
2 1867 5190 225 795 1642 4395 2059 5542 228 818 1834 4747 0 0 1039 3079 36 243 97 86 94 83 6037 6581 .374 2.677 2.588 1 1 1 120 342 1 .96 130 1870 8750 28 41 32 45 0 8508 1303 7205 4.388 9085 7782 .228 4.243 2.134 2.085
3 576 1277 223 744 353 533 397 938 227 781 174 194 0 0 372 794 38 362 80 41 65 33 886 368 .662 1.51 1.115 1 1 1 120 346 1 .76 130 2030 8750 28 41 48 61 0 2093 1220 874 2.475 1538 318 .404 1.828 1.308 .87
4 547 1201 220 649 327 552 478 1026 220 687 258 377 0 0 340 832 34 329 70 50 63 39 879 635 .592 1.688 1.461 1 1 1 120 358 1 .73 130 2170 8750 28 41 62 75 0 1969 1064 905 2.767 1682 618 .361 2.395 1.468 1.26
5 984 1968 218 688 766 1280 641 1391 218 693 423 703 0 0 770 1373 33 183 92 77 82 65 2046 1126 .598 1.671 1.662 1 1 1 80 226 1 .96 100 2320 8750 30 40 79 89 0 3226 1128 2098 2.739 2280 1152 .365 2.724 1.454 1.446
6 448 1172 213 733 235 439 289 870 265 871 76 137 0 0 317 702 560 1671 20 9 1 0 674 213 .535 1.868 1.803 1 1 1 120 341 1 .92 130 2460 8760 29 42 91 104 0 1921 1202 720 3.062 1426 225 .327 2.955 1.615 1.563
7 1556 6461 215 723 1341 5738 1160 4185 275 858 945 3462 0 0 1323 5896 590 1756 58 64 43 50 7079 4407 .234 4.279 3.663 1 1 1 120 307 1 .96 120 2610 8750 29 41 107 119 0 10592 1185 9407 7.015 6861 5675 .143 6.006 2.81 2.586
8 3268 2092 218 723 3050 1369 3263 2144 222 745 3045 1421 0 0 1798 910 37 168 99 85 99 84 4419 4466 2.228 .449 .467 1 1 1 120 345 1 .94 130 2760 8750 28 41 121 134 0 3430 1185 2244 .736 3515 2330 1.359 .765 -.443 -.386
9 1017 1915 223 759 794 1156 1013 2074 226 788 790 1315 0 0 622 944 38 201 90 74 85 69 1950 2105 .687 1.456 1.665 1 1 1 120 345 1 .9 130 2910 8750 28 41 136 149 0 3139 1244 1895 2.387 3400 2156 .419 2.729 1.255 1.448
10 574 1329 233 778 341 551 530 1311 234 821 297 533 0 0 316 631 44 232 71 59 61 53 892 830 .619 1.616 1.795 1 1 1 120 346 1 .86 130 3060 8750 28 41 151 164 0 2179 1275 903 2.649 2149 874 .378 2.942 1.405 1.557
11 27832 4206 234 761 27598 3445 33665 4748 239 793 33431 3987 0 0 20269 2542 44 236 100 85 100 79 31043 37418 8.011 .125 .119 1 1 1 120 343 1 .97 130 3200 8750 28 41 165 178 0 6895 1248 5648 .205 7784 6536 4.887 .196 -2.289 -2.355
12 5221 3240 234 763 4987 2477 4633 3058 242 791 4399 2295 0 0 4732 2223 47 213 91 76 85 71 7464 6694 2.013 .497 .522 1 1 1 120 305 1 .97 120 3340 8750 29 41 180 192 0 5311 1251 4061 .814 5013 3762 1.228 .855 -.296 -.226
13 2811 1727 233 759 2578 968 2860 1756 239 785 2627 997 0 0 2151 799 43 235 89 72 88 64 3546 3624 2.663 .375 .38 1 1 1 120 355 1 .92 130 3490 8750 28 41 194 207 0 2831 1244 1587 .616 2879 1634 1.625 .622 -.7 -.685
14 1258 2174 239 726 1019 1448 1403 2264 242 757 1164 1538 0 0 484 869 42 237 95 85 93 82 2467 2702 .704 1.421 1.321 1 1 1 120 347 1 .92 130 3650 8750 28 41 210 223 0 3564 1190 2374 2.33 3711 2521 .429 2.166 1.22 1.115
15 380 1035 236 726 144 309 275 933 240 747 39 207 0 0 379 416 40 197 49 52 31 30 453 246 .466 2.146 5.308 1 1 1 120 333 1 .6 130 3790 8750 28 41 224 237 0 1697 1190 507 3.518 1530 339 .284 8.701 1.815 3.121
16 2915 3202 230 720 2685 2482 2764 3075 229 735 2534 2355 0 0 2159 2040 36 187 87 79 85 74 5167 4889 1.082 .924 .929 1 1 1 120 274 1 .96 120 3930 8750 29 41 239 251 0 5249 1180 4069 1.515 5041 3861 .66 1.524 .6 .607
17 6679 4398 233 733 6446 3665 6627 4576 234 738 6394 3843 0 0 4412 2674 37 182 93 83 92 83 10111 10237 1.759 .569 .601 1 1 1 156 433 1 .98 140 4070 8750 28 42 252 266 0 7210 1202 6008 .932 7502 6300 1.073 .985 -.101 -.021
18 401 1183 235 754 166 429 315 962 242 773 80 208 0 0 286 614 50 202 65 50 38 33 595 288 .387 2.584 2.6 1 1 1 120 369 1 .73 130 4240 8740 27 40 269 282 0 1939 1236 703 4.237 1577 341 .236 4.262 2.083 2.092
19 17385 14651 241 783 17144 13868 17509 16491 246 801 17268 15708 0 0 11238 8805 50 188 99 95 98 92 31012 32976 1.236 .809 .91 1 1 1 120 337 1 .98 130 4370 8750 28 41 282 295 0 24018 1284 22734 1.326 27034 25751 .754 1.491 .407 .577
20 4471 5274 240 772 4231 4502 4842 5955 243 785 4602 5183 0 0 2078 2180 40 175 99 95 97 93 8733 9785 .94 1.064 1.126 1 1 1 120 359 1 .97 130 4510 8750 28 41 296 309 0 8646 1266 7380 1.744 9762 8497 .573 1.846 .803 .885

Total number of rows: 43008

Table truncated, full table size 9065 Kbytes.




Supplementary data files not provided
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