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Sample GSM71841 Query DataSets for GSM71841
Status Public on Aug 25, 2005
Title AD50 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 50 hpi
Organism Homo sapiens
Characteristics AD169 50 hpi
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Virus, Cytomegalovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31131.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
1 799 1016 490 553 309 463 676 771 495 578 186 218 0 0 432 664 98 151 61 56 48 45 772 404 .667 1.498 1.172 1 1 1 120 553 1 .81 130 1610 9460 31 44 34 47 0 1847 1005 842 2.724 1402 396 .367 2.131 1.446 1.092
2 1581 1756 492 561 1089 1195 988 1141 507 580 496 580 0 0 1301 1445 99 151 68 70 60 57 2284 1076 .911 1.097 1.169 1 1 1 120 343 1 .92 130 1750 9460 31 44 48 61 0 3193 1020 2173 1.995 2075 1055 .501 2.126 .997 1.088
3 782 1008 505 568 277 440 645 761 510 575 140 193 0 0 448 693 102 151 57 53 43 40 717 333 .63 1.588 1.379 1 1 1 120 343 1 .84 130 1900 9460 31 44 63 76 0 1833 1033 800 2.888 1384 351 .346 2.506 1.53 1.326
4 1100 1392 515 586 585 806 1171 1487 524 605 656 901 0 0 503 711 117 166 76 77 71 70 1391 1557 .726 1.378 1.373 1 1 1 120 343 1 .85 130 2040 9460 31 44 77 90 0 2531 1065 1465 2.505 2704 1638 .399 2.497 1.325 1.32
5 910 1062 507 579 403 483 623 749 516 590 116 170 0 0 722 821 114 155 50 52 37 39 886 286 .834 1.199 1.466 1 1 1 120 356 1 .82 130 2190 9460 31 44 92 105 0 1931 1053 878 2.179 1362 309 .459 2.665 1.124 1.414
6 695 957 486 547 209 410 553 662 491 565 67 115 0 0 429 710 100 198 45 39 31 30 619 182 .51 1.962 1.716 1 1 1 120 343 1 .77 130 2340 9460 31 44 107 120 0 1740 995 745 3.567 1204 209 .28 3.121 1.835 1.642
7 1559 2233 469 517 1090 1716 763 1171 479 542 294 654 0 0 1536 2237 98 189 70 67 59 55 2806 948 .635 1.574 2.224 1 1 1 120 343 1 .91 130 2480 9460 31 44 121 134 0 4060 940 3120 2.862 2129 1189 .349 4.045 1.517 2.016
8 3493 1802 474 526 3019 1276 3498 1878 479 542 3024 1352 0 0 2880 940 98 136 89 86 87 83 4295 4376 2.366 .423 .447 1 1 1 120 343 1 .81 130 2630 9460 31 44 136 149 0 3276 956 2320 .768 3415 2458 1.301 .813 -.38 -.299
9 1342 1545 474 535 868 1010 1018 1318 478 552 544 783 0 0 973 1002 97 146 68 72 62 65 1878 1327 .859 1.164 1.439 1 1 1 120 343 1 .89 130 2770 9460 31 44 150 163 0 2809 973 1836 2.116 2396 1424 .473 2.617 1.081 1.388
10 850 1238 469 552 381 686 642 958 476 564 173 406 0 0 499 851 100 139 61 62 45 55 1067 579 .555 1.801 2.347 1 1 1 120 343 1 .85 130 2920 9460 31 44 165 178 0 2251 1004 1247 3.274 1742 738 .305 4.267 1.711 2.093
11 23483 2182 445 525 23038 1657 19952 2296 453 546 19507 1771 0 0 19676 1566 95 164 95 73 94 65 24695 21278 13.903 .072 .091 1 1 1 120 343 1 .91 130 3060 9460 31 44 179 192 0 3967 955 3013 .131 4175 3220 7.647 .165 -2.935 -2.599
12 5128 2042 441 520 4687 1522 2206 1484 449 537 1765 964 0 0 5614 1610 95 159 81 70 75 61 6209 2729 3.08 .325 .546 1 1 1 120 343 1 .89 130 3210 9460 31 44 194 207 0 3713 945 2767 .59 2698 1753 1.694 .993 -.76 -.01
13 2855 1668 448 541 2407 1127 2236 1409 457 548 1788 868 0 0 2394 1163 96 148 77 71 73 65 3534 2656 2.136 .468 .485 1 1 1 120 343 1 .9 130 3350 9460 31 44 208 221 0 3033 984 2049 .851 2562 1578 1.175 .883 -.232 -.18
14 1600 1576 433 528 1167 1048 1785 1724 447 541 1352 1196 0 0 807 701 95 129 85 83 81 80 2215 2548 1.114 .898 .885 1 1 1 120 343 1 .87 130 3500 9460 31 44 223 236 0 2865 960 1905 1.633 3135 2175 .612 1.608 .707 .686
15 2092 2263 422 533 1670 1730 558 782 432 549 136 249 1 1 9406 8687 89 134 51 56 41 47 3400 385 .965 1.036 1.831 1 1 1 120 343 1 .98 130 3640 9460 31 44 237 250 0 4115 969 3145 1.884 1422 453 .531 3.329 .913 1.735
16 2893 2799 435 533 2458 2266 1461 1757 444 551 1026 1224 0 0 2985 2472 96 131 72 73 64 67 4724 2250 1.085 .922 1.193 1 1 1 120 341 1 .94 130 3790 9460 31 44 252 265 0 5089 969 4120 1.676 3195 2225 .597 2.169 .745 1.117
17 14049 6196 446 560 13603 5636 15426 6728 456 577 14980 6168 0 0 7703 3247 96 150 100 92 100 90 19239 21148 2.414 .414 .412 1 1 1 120 357 1 .96 130 3940 9450 30 43 267 280 0 11265 1018 10247 .753 12233 11215 1.327 .749 -.409 -.418
18 471 668 438 560 33 108 474 616 450 574 36 56 0 0 258 391 90 139 37 37 17 20 141 92 .306 3.273 1.556 1 1 1 120 345 1 .62 130 4080 9460 31 44 281 294 0 1215 1018 196 5.95 1120 102 .168 2.828 2.573 1.5
19 20749 17918 441 569 20308 17349 16891 17063 456 586 16450 16494 0 0 19309 15576 100 148 95 97 90 90 37657 32944 1.171 .854 1.003 1 1 1 120 347 1 .99 130 4230 9460 31 44 296 309 0 32578 1035 31544 1.553 31024 29989 .644 1.823 .635 .866
20 5479 5238 454 548 5025 4690 4598 5024 463 574 4144 4476 0 0 4302 3657 102 156 87 87 80 80 9715 8620 1.071 .933 1.08 1 1 1 120 328 1 .96 130 4370 9460 31 44 310 323 0 9524 996 8527 1.697 9135 8138 .589 1.964 .763 .974

Total number of rows: 43008

Table truncated, full table size 9239 Kbytes.




Supplementary data files not provided
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