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Sample GSM71840 Query DataSets for GSM71840
Status Public on Aug 25, 2005
Title AD72 hpi 1
Sample type RNA
 
Channel 1
Source name Mock
Organism Homo sapiens
Characteristics Mock
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name AD169 72 hpi
Organism Homo sapiens
Characteristics AD169 72 hpi
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31791.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) 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 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
1 213 393 87 209 126 184 173 306 87 215 86 97 0 0 126 212 14 53 71 56 60 50 310 183 .685 1.46 1.128 1 1 1 120 553 1 .9 130 1680 8880 21 34 25 38 0 624 332 292 2.318 486 154 .431 1.79 1.213 .84
2 360 705 85 193 275 512 426 790 86 198 341 597 0 0 224 436 13 43 78 71 72 68 787 938 .537 1.862 1.751 1 1 1 120 343 1 .98 130 1820 8880 21 34 39 52 0 1119 306 813 2.955 1254 948 .338 2.779 1.563 1.475
3 196 402 81 179 115 223 142 289 82 184 61 110 0 0 123 244 13 37 73 70 65 58 338 171 .516 1.939 1.803 1 1 1 120 343 1 .93 130 1970 8880 21 34 54 67 0 638 284 354 3.078 459 175 .325 2.862 1.622 1.517
4 196 395 79 180 117 215 163 311 81 184 84 131 0 0 112 244 14 37 75 64 66 56 332 215 .544 1.838 1.56 1 1 1 120 352 1 .9 130 2110 8880 21 34 68 81 0 627 286 341 2.917 494 208 .343 2.475 1.544 1.308
5 357 541 82 187 275 354 284 501 84 191 202 314 0 0 236 268 14 40 92 88 85 82 629 516 .777 1.287 1.554 1 1 1 80 242 1 .95 100 2250 8880 23 33 84 94 0 859 297 562 2.043 795 498 .489 2.467 1.031 1.303
6 146 456 77 178 69 278 98 275 79 182 21 97 0 0 105 384 12 34 65 72 45 55 347 118 .248 4.029 4.619 1 1 1 120 376 1 .92 130 2410 8880 21 34 98 111 0 724 283 441 6.395 437 154 .156 7.332 2.677 2.874
7 527 1322 81 186 446 1136 535 1388 83 189 454 1202 0 0 362 878 15 38 84 84 75 78 1582 1656 .393 2.547 2.648 1 1 1 120 340 1 .98 130 2550 8880 21 34 112 125 0 2098 295 1803 4.043 2203 1908 .247 4.203 2.015 2.071
8 487 430 85 193 402 237 463 408 86 196 378 215 0 0 335 202 16 42 92 79 85 70 639 593 1.696 .59 .569 1 1 1 120 348 1 .88 130 2690 8880 21 34 126 139 0 683 306 376 .936 648 341 1.069 .903 -.096 -.147
9 465 785 82 198 383 587 433 681 84 201 351 483 0 0 314 504 17 44 90 87 81 77 970 834 .652 1.533 1.376 1 1 1 120 350 1 .98 130 2840 8880 21 34 141 154 0 1246 314 932 2.433 1081 767 .411 2.184 1.283 1.127
10 278 602 82 186 196 416 193 433 83 191 111 247 0 0 222 469 15 44 79 75 70 67 612 358 .471 2.122 2.225 1 1 1 120 349 1 .97 130 2990 8880 21 34 156 169 0 956 295 660 3.369 687 392 .297 3.532 1.752 1.821
11 10607 1079 77 173 10530 906 12123 1223 79 177 12046 1050 0 0 7786 681 13 38 100 98 100 91 11436 13096 11.623 .086 .087 1 1 1 120 350 1 .98 130 3130 8880 21 34 170 183 0 1713 275 1438 .137 1941 1667 7.322 .138 -2.872 -2.854
12 1905 1496 78 177 1827 1319 1400 609 79 182 1322 432 0 0 1802 2132 13 41 86 76 81 70 3146 1754 1.385 .722 .327 1 1 1 120 343 1 .62 130 3280 8880 21 34 185 198 0 2375 281 2094 1.146 967 686 .873 .519 .197 -.947
13 546 406 79 182 467 224 589 441 79 184 510 259 0 0 360 157 13 37 92 81 85 75 691 769 2.085 .48 .508 1 1 1 120 328 1 .89 130 3420 8880 21 34 199 212 0 644 289 356 .761 700 411 1.313 .806 -.393 -.311
14 660 845 79 182 581 663 562 679 79 184 483 497 0 0 441 555 13 37 90 86 90 85 1244 980 .876 1.141 1.029 1 1 1 120 360 1 .96 130 3560 8870 20 33 213 226 0 1341 289 1052 1.811 1078 789 .552 1.633 .857 .708
15 98 242 76 173 22 69 92 233 78 182 16 60 0 0 31 78 13 69 54 43 35 17 91 76 .319 3.136 3.75 1 1 1 120 344 1 .63 130 3710 8880 21 34 228 241 0 384 275 110 4.978 370 95 .201 5.952 2.316 2.573
16 809 802 73 154 736 648 705 691 74 164 632 537 0 0 687 621 14 72 88 77 82 74 1384 1169 1.136 .88 .85 1 1 1 120 340 1 .98 130 3860 8880 21 34 243 256 0 1273 244 1029 1.398 1097 852 .716 1.349 .483 .432
17 2125 1368 70 132 2055 1236 2589 1606 71 135 2519 1474 0 0 1006 631 11 30 96 95 93 91 3291 3993 1.663 .601 .585 1 1 1 120 385 1 .98 130 4000 8870 20 33 257 270 0 2171 210 1962 .955 2549 2340 1.047 .929 -.067 -.107
18 77 160 73 146 4 14 72 148 73 149 -1 2 0 0 21 56 12 37 20 26 10 10 18 1 .286 3.5 null 1 1 1 120 357 1 .33 130 4150 8880 21 34 272 285 0 254 232 22 5.556 235 3 .18 null 2.474 null
19 2657 2201 73 151 2584 2050 2977 2488 74 154 2904 2337 0 0 2132 1677 12 34 89 81 84 79 4634 5241 1.26 .793 .805 1 1 1 120 355 1 .99 130 4290 8870 20 33 286 299 0 3494 240 3254 1.259 3949 3710 .794 1.277 .333 .353
20 967 976 73 152 894 824 1036 1051 74 156 963 899 0 0 569 549 12 34 90 84 88 82 1718 1862 1.085 .922 .934 1 1 1 120 348 1 .98 130 4440 8870 20 33 301 314 0 1549 241 1308 1.463 1668 1427 .684 1.482 .549 .567

Total number of rows: 43008

Table truncated, full table size 8820 Kbytes.




Supplementary data files not provided
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