NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM71846 Query DataSets for GSM71846
Status Public on Aug 25, 2005
Title RV50 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 50 hpi
Organism Homo sapiens
Characteristics RV101 50 hpi
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31128.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 1025 803 666 700 359 103 877 781 675 720 211 81 0 0 412 200 131 179 62 35 44 11 462 292 3.485 .287 .384 1 1 1 120 548 1 .49 130 1630 8960 53 66 24 37 0 1295 1129 166 .463 1260 131 2.161 .619 -1.112 -.692
2 2865 1907 687 701 2178 1206 2781 1722 696 718 2094 1021 0 0 1978 1147 117 146 79 73 70 62 3384 3115 1.806 .554 .488 1 1 1 120 337 1 .91 130 1770 8960 53 66 38 51 0 3076 1131 1945 .893 2777 1647 1.12 .786 -.163 -.347
3 967 908 696 717 271 191 884 844 699 725 188 127 0 0 340 295 114 145 56 44 41 30 462 315 1.419 .705 .676 1 1 1 120 354 1 .69 130 1920 8950 52 65 53 66 0 1465 1156 308 1.137 1361 205 .88 1.09 .185 .124
4 1078 954 706 712 372 242 916 900 713 723 210 188 0 0 441 282 114 144 62 53 49 37 614 398 1.537 .651 .895 1 1 1 120 349 1 .73 130 2060 8950 52 65 67 80 0 1539 1148 390 1.049 1452 303 .953 1.444 .069 .53
5 850 830 645 669 205 161 683 707 619 669 38 38 0 0 492 368 172 145 35 37 25 29 366 76 1.273 .785 1 1 1 1 120 352 1 .83 130 2210 8950 52 65 82 95 0 1339 1079 260 1.267 1140 61 .789 1.613 .341 .69
6 935 842 633 695 302 147 782 738 610 702 149 43 0 0 429 358 170 180 44 31 24 16 449 192 2.054 .487 .289 1 1 1 120 340 1 .71 130 2360 8950 52 65 97 110 0 1358 1121 237 .785 1190 69 1.274 .465 -.349 -1.103
7 1411 1709 614 683 797 1026 1095 1347 612 704 481 664 0 0 957 1295 258 260 57 62 48 55 1823 1145 .777 1.287 1.38 1 1 1 120 343 1 .89 130 2500 8950 52 65 111 124 0 2756 1102 1655 2.076 2173 1071 .482 2.227 1.054 1.155
8 4884 1490 627 675 4257 815 5617 1558 624 691 4990 883 0 0 2442 540 256 238 91 78 87 68 5072 5873 5.223 .191 .177 1 1 1 120 337 1 .87 130 2650 8950 52 65 126 139 0 2403 1089 1315 .309 2513 1424 3.238 .285 -1.695 -1.809
9 1945 1475 637 696 1308 779 1979 1476 631 708 1342 780 0 0 971 616 161 158 79 76 74 68 2087 2122 1.679 .596 .581 1 1 1 120 356 1 .93 130 2790 8940 51 64 140 153 0 2379 1123 1256 .961 2381 1258 1.041 .937 -.058 -.093
10 1200 1057 634 692 566 365 972 911 629 709 338 219 0 0 666 458 163 159 62 59 50 40 931 557 1.551 .645 .648 1 1 1 120 350 1 .85 130 2940 8940 51 64 155 168 0 1705 1116 589 1.04 1469 353 .961 1.045 .057 .064
11 24450 1935 673 708 23777 1227 28995 2095 663 716 28322 1387 0 0 17016 890 135 145 94 79 87 72 25004 29709 19.378 .052 .049 1 1 1 120 345 1 .96 130 3080 8940 51 64 169 182 0 3121 1142 1979 .083 3379 2237 12.014 .079 -3.587 -3.662
12 7684 2675 659 706 7025 1969 5142 2477 660 710 4483 1771 0 0 7269 2027 140 158 80 73 72 65 8994 6254 3.568 .28 .395 1 1 1 120 341 1 .93 130 3230 8940 51 64 184 197 0 4315 1139 3176 .452 3995 2856 2.212 .637 -1.145 -.65
13 5011 1770 676 741 4335 1029 4131 1592 685 749 3455 851 0 0 3815 911 110 142 84 75 75 67 5364 4306 4.213 .237 .246 1 1 1 120 337 1 .9 130 3370 8940 51 64 198 211 0 2855 1195 1660 .383 2568 1373 2.612 .397 -1.385 -1.332
14 3045 1884 657 730 2388 1154 3304 2068 666 740 2647 1338 0 0 1311 715 108 133 90 85 87 81 3542 3985 2.069 .483 .505 1 1 1 120 354 1 .93 130 3520 8930 50 63 213 226 0 3039 1177 1861 .779 3335 2158 1.283 .815 -.359 -.295
15 968 825 675 730 293 95 761 764 682 738 86 34 0 0 528 240 109 129 47 34 31 20 388 120 3.084 .324 .395 1 1 1 120 358 1 .51 130 3660 8930 50 63 227 240 0 1331 1177 153 .523 1232 55 1.912 .638 -.935 -.649
16 4904 3243 690 740 4214 2503 4497 3267 698 752 3807 2527 0 0 3618 2075 122 131 85 80 79 73 6717 6334 1.684 .594 .664 1 1 1 120 346 1 .95 130 3820 8930 50 63 243 256 0 5231 1194 4037 .958 5269 4076 1.044 1.071 -.062 .098
17 15959 5170 691 759 15268 4411 16316 5247 702 769 15625 4488 0 0 9905 2996 122 129 98 94 95 92 19679 20113 3.461 .289 .287 1 1 1 120 325 1 .95 130 3960 8930 50 63 257 270 0 8339 1224 7115 .466 8463 7239 2.146 .463 -1.102 -1.11
18 799 840 626 732 173 108 739 789 621 736 113 57 0 0 300 336 150 145 43 30 16 15 281 170 1.602 .624 .504 1 1 1 120 342 1 .48 130 4100 8930 50 63 271 284 0 1355 1181 174 1.007 1273 92 .993 .814 .01 -.298
19 19318 12394 614 728 18704 11666 20064 14270 612 731 19450 13542 0 0 14721 8352 158 152 95 95 93 95 30370 32992 1.603 .624 .696 1 1 1 120 340 1 .95 130 4250 8930 50 63 286 299 0 19990 1174 18816 1.006 23016 21842 .994 1.123 .009 .167
20 5356 3828 656 780 4700 3048 6203 4330 673 782 5547 3550 0 0 3343 2156 124 147 88 84 84 81 7748 9097 1.542 .649 .64 1 1 1 120 356 1 .94 130 4390 8920 49 62 300 313 0 6174 1258 4916 1.046 6984 5726 .956 1.032 .065 .046

Total number of rows: 43008

Table truncated, full table size 9184 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap