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Sample GSM71842 Query DataSets for GSM71842
Status Public on Aug 25, 2005
Title RV72 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 RV101 72 hpi
Organism Homo sapiens
Characteristics RV101 72 hpi
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31947.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
1 245 692 138 480 107 212 204 595 141 492 66 115 0 0 112 306 29 100 61 51 53 45 319 181 .505 1.981 1.742 1 1 1 120 529 1 .78 130 1740 9010 38 51 19 32 0 935 649 286 2.677 804 155 .373 2.355 1.421 1.235
2 481 1233 136 459 345 774 541 1344 137 462 405 885 0 0 244 592 28 95 81 80 75 73 1119 1290 .446 2.243 2.185 1 1 1 120 337 1 .91 130 1880 9010 38 51 33 46 0 1666 620 1046 3.032 1816 1196 .33 2.953 1.6 1.562
3 239 640 133 444 106 196 206 539 137 446 73 95 0 0 115 324 28 94 62 50 54 39 302 168 .541 1.849 1.301 1 1 1 120 356 1 .79 130 2030 9000 37 50 48 61 0 865 600 265 2.499 728 128 .4 1.759 1.321 .814
4 231 655 131 421 100 234 219 591 134 426 88 170 0 0 86 269 27 103 75 57 65 46 334 258 .427 2.34 1.932 1 1 1 120 365 1 .68 130 2170 9000 37 50 62 75 0 885 569 316 3.162 799 230 .316 2.611 1.661 1.384
5 432 895 128 387 304 508 419 846 131 397 291 459 0 0 248 423 27 89 80 78 72 68 812 750 .598 1.671 1.577 1 1 1 80 241 1 .89 100 2320 9000 39 49 79 89 0 1209 523 686 2.258 1143 620 .443 2.132 1.175 1.092
6 160 568 128 365 32 203 144 423 131 368 16 58 0 0 67 348 27 85 40 43 25 30 235 74 .158 6.344 3.625 1 1 1 120 375 1 .73 130 2470 9000 37 50 92 105 0 768 493 274 8.573 572 78 .117 4.899 3.1 2.292
7 677 2072 142 364 535 1708 640 2023 144 365 498 1659 0 0 470 1508 32 93 80 73 73 70 2243 2157 .313 3.193 3.331 1 1 1 120 306 1 .95 120 2620 9000 38 50 108 120 0 2800 492 2308 4.314 2734 2242 .232 4.502 2.109 2.17
8 831 848 137 364 694 484 899 893 139 371 762 529 0 0 337 290 33 89 97 90 94 81 1178 1291 1.434 .697 .694 1 1 1 120 356 1 .84 130 2770 9000 37 50 122 135 0 1146 492 654 .942 1207 715 1.061 .938 -.086 -.092
9 443 996 126 337 317 659 484 1004 128 342 358 667 0 0 228 537 27 76 86 81 77 75 976 1025 .481 2.079 1.863 1 1 1 120 345 1 .92 130 2920 9000 37 50 137 150 0 1346 455 891 2.809 1357 901 .356 2.518 1.49 1.332
10 283 822 131 340 152 482 238 656 133 344 107 316 0 0 157 464 26 81 70 78 62 65 634 423 .315 3.171 2.953 1 1 1 120 355 1 .89 130 3070 8990 36 49 152 165 0 1111 459 651 4.285 886 427 .233 3.991 2.099 1.997
11 10643 1467 133 338 10510 1129 13672 1516 135 342 13539 1178 0 0 6323 816 27 79 99 90 97 83 11639 14717 9.309 .107 .087 1 1 1 120 306 1 .92 120 3210 8990 37 49 167 179 0 1982 457 1526 .145 2049 1592 6.889 .118 -2.784 -3.088
12 2591 1683 127 332 2464 1351 2389 1364 129 337 2262 1032 0 0 2208 1314 27 82 86 82 84 73 3815 3294 1.824 .548 .456 1 1 1 120 310 1 .96 120 3360 8990 37 49 182 194 0 2274 449 1826 .741 1843 1395 1.35 .617 -.433 -.698
13 957 801 126 324 831 477 897 754 129 331 771 430 0 0 632 414 27 82 90 72 83 67 1308 1201 1.742 .574 .558 1 1 1 120 340 1 .9 130 3500 8990 36 49 195 208 0 1082 438 645 .776 1019 581 1.289 .754 -.366 -.408
14 652 1304 127 331 525 973 597 1176 128 336 470 845 0 0 434 845 29 77 87 85 83 79 1498 1315 .54 1.853 1.798 1 1 1 120 364 1 .95 130 3640 8980 35 48 209 222 0 1762 447 1315 2.505 1589 1142 .399 2.43 1.325 1.281
15 145 377 122 316 23 61 137 351 124 316 15 35 0 0 41 123 26 77 37 33 20 19 84 50 .377 2.652 2.333 1 1 1 120 338 1 .39 130 3790 8990 36 49 224 237 0 509 427 82 3.584 474 47 .279 3.153 1.842 1.657
16 1543 1767 120 277 1423 1490 1572 1672 124 286 1452 1395 0 0 1149 1322 26 70 92 85 86 79 2913 2847 .955 1.047 .961 1 1 1 120 361 1 .97 130 3940 8980 35 48 239 252 0 2388 374 2014 1.415 2259 1885 .707 1.298 .501 .377
17 3245 3166 130 267 3115 2899 3458 3273 132 276 3328 3006 0 0 1291 1524 28 70 99 96 97 93 6014 6334 1.075 .931 .903 1 1 1 120 379 1 .96 130 4090 8980 35 48 254 267 0 4278 361 3918 1.258 4423 4062 .795 1.221 .331 .288
18 154 301 133 279 21 22 144 278 134 286 11 -1 0 0 53 108 27 81 32 24 13 10 43 10 .955 1.048 null 1 1 1 120 375 1 .29 130 4230 8980 35 48 268 281 0 407 377 30 1.416 376 null .706 null .502 null
19 3778 4377 138 300 3640 4077 4509 5220 140 305 4371 4920 0 0 2035 2362 31 77 98 96 95 90 7717 9291 .893 1.12 1.126 1 1 1 120 371 1 .97 130 4380 8980 35 48 283 296 0 5915 405 5509 1.514 7054 6649 .661 1.521 .598 .605
20 1450 1881 136 304 1314 1577 1532 1928 138 310 1396 1624 0 0 815 1073 30 75 95 90 88 85 2891 3020 .833 1.2 1.163 1 1 1 120 377 1 .97 130 4520 8980 35 48 297 310 0 2542 411 2131 1.622 2605 2195 .617 1.572 .698 .653

Total number of rows: 43008

Table truncated, full table size 8947 Kbytes.




Supplementary data files not provided
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