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Sample GSM71843 Query DataSets for GSM71843
Status Public on Aug 25, 2005
Title RV50 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 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/2002-07/31125.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 2072 2620 1235 2332 837 288 1675 2693 1262 2390 440 361 0 0 969 893 228 517 70 37 49 18 1125 801 2.906 .344 .82 1 1 1 120 553 1 .55 130 1970 9000 37 50 38 51 0 4295 3823 472 .564 4415 592 1.773 1.345 -.826 .428
2 3448 3970 1213 2235 2235 1735 3289 3708 1247 2328 2076 1473 0 0 1949 1593 228 470 76 70 66 56 3970 3549 1.288 .776 .71 1 1 1 120 343 1 .89 130 2110 9000 37 50 52 65 0 6508 3664 2844 1.273 6079 2415 .786 1.163 .348 .218
3 1783 2627 1222 2217 561 410 1379 2428 1237 2294 157 211 0 0 1049 1148 253 507 41 36 31 25 971 368 1.368 .731 1.344 1 1 1 120 343 1 .77 130 2260 9000 37 50 67 80 0 4307 3634 672 1.198 3980 346 .835 2.203 .261 1.14
4 2224 2865 1255 2367 969 498 2259 2908 1580 3049 1004 541 0 0 924 1025 3689 5577 0 0 0 0 1467 1545 1.946 .514 .539 1 1 1 120 352 1 .67 130 2400 9000 37 50 81 94 0 4697 3880 816 .843 4767 887 1.187 .883 -.247 -.179
5 3248 3237 1256 2480 1992 757 1688 2652 1728 3401 432 172 0 0 2773 2115 4441 6694 25 0 1 0 2749 604 2.631 .38 .398 1 1 1 80 242 1 .66 100 2540 9000 39 49 97 107 0 5307 4066 1241 .623 4348 282 1.605 .653 -.683 -.616
6 1596 2503 1199 2289 397 214 1157 2181 1215 2314 -42 -108 0 0 1200 1441 227 449 30 28 24 20 611 -150 1.855 .539 null 1 1 1 120 376 1 .81 130 2700 9000 37 50 111 124 0 4103 3752 351 .884 3575 null 1.132 null -.178 null
7 4102 7170 1133 2081 2969 5089 2109 3748 1148 2134 976 1667 0 0 3639 6242 206 397 66 74 57 60 8058 2643 .583 1.714 1.708 1 1 1 120 340 1 .97 130 2840 9000 37 50 125 138 0 11754 3411 8343 2.81 6144 2733 .356 2.8 1.491 1.485
8 6182 3389 1118 1956 5064 1433 7076 3675 1137 2000 5958 1719 0 0 2894 1320 191 351 90 79 89 75 6497 7677 3.534 .283 .289 1 1 1 120 348 1 .84 130 2980 9000 37 50 139 152 0 5556 3207 2349 .464 6025 2818 2.156 .473 -1.108 -1.08
9 4145 3659 1128 1992 3017 1667 4168 3539 1153 2023 3040 1547 0 0 2468 1623 181 376 80 69 77 65 4684 4587 1.81 .553 .509 1 1 1 120 344 1 .9 130 3130 9000 37 50 154 167 0 5998 3266 2733 .906 5802 2536 1.104 .834 -.143 -.261
10 2067 2897 1156 2073 911 824 1534 2630 1174 2103 378 557 0 0 1235 1481 197 413 55 52 49 40 1735 935 1.106 .905 1.474 1 1 1 120 346 1 .85 130 3280 9000 37 50 169 182 0 4749 3398 1351 1.483 4311 913 .674 2.416 .568 1.272
11 45518 5665 1188 2218 44330 3447 65535 6481 1201 2239 64347 4263 53 0 25919 2994 207 419 97 77 97 70 47777 68610 12.86 .078 .066 1 1 1 120 352 1 .9 130 3420 9000 37 50 183 196 0 9287 3636 5651 .127 10625 6989 7.845 .109 -2.972 -3.203
12 13473 6255 1155 2117 12318 4138 8872 5115 1168 2161 7717 2998 0 0 13531 4919 212 417 80 63 75 58 16456 10715 2.977 .336 .388 1 1 1 120 343 1 .95 130 3570 9000 37 50 198 211 0 10254 3470 6784 .551 8385 4915 1.816 .637 -.861 -.651
13 6694 3826 1094 2002 5600 1824 4233 2975 1106 2021 3139 973 0 0 6047 2418 192 378 73 58 70 52 7424 4112 3.07 .326 .31 1 1 1 120 328 1 .93 130 3710 9000 37 50 212 225 0 6272 3282 2990 .534 4877 1595 1.873 .508 -.905 -.977
14 7441 5243 1161 2140 6280 3103 8186 5656 1189 2207 7025 3516 0 0 3203 2061 212 493 95 85 94 82 9383 10541 2.024 .494 .5 1 1 1 120 360 1 .91 130 3850 8990 36 49 226 239 0 8595 3508 5087 .81 9272 5764 1.235 .82 -.304 -.285
15 1433 2065 1187 2236 246 -171 1232 2049 1197 2261 45 -187 0 0 881 950 206 494 30 24 25 11 75 -142 null null null 1 1 1 120 344 1 .63 130 4000 9000 37 50 241 254 0 3385 3666 -280 null 3359 null null null null null
16 8214 7464 1200 2200 7014 5264 5762 6422 1202 2227 4562 4222 0 0 6891 5209 203 400 85 79 79 70 12278 8784 1.332 .75 .925 1 1 1 120 334 1 .96 130 4150 9000 37 50 256 269 0 12236 3607 8630 1.23 10528 6921 .813 1.517 .299 .601
17 17705 8702 1235 2238 16470 6464 17194 8351 1237 2247 15959 6113 0 0 8680 4083 208 420 99 90 98 90 22934 22072 2.548 .392 .383 1 1 1 120 358 1 .95 130 4290 8990 36 49 270 283 0 14266 3669 10597 .643 13690 10021 1.554 .628 -.636 -.671
18 1304 2164 1219 2164 85 0 1202 2099 1223 2186 -17 -65 0 0 712 931 218 429 27 27 15 12 85 -82 null null null 1 1 1 120 339 1 .58 130 4440 9000 37 50 285 298 0 3548 3548 0 null 3441 null null null null null
19 33430 28154 1211 2162 32219 25992 32594 26636 1215 2187 31383 24474 25 0 26370 21627 225 455 88 87 85 83 58211 55857 1.24 .807 .78 1 1 1 120 359 1 .97 130 4580 8990 36 49 299 312 0 46154 3544 42610 1.323 43666 40121 .756 1.278 .403 .354
20 12153 10714 1232 2201 10921 8513 13627 12158 1239 2249 12395 9957 0 0 5641 4947 235 464 95 90 95 87 19434 22352 1.283 .78 .803 1 1 1 120 348 1 .96 130 4730 8990 36 49 314 327 0 17564 3608 13956 1.278 19931 16323 .783 1.317 .354 .397

Total number of rows: 43008

Table truncated, full table size 9481 Kbytes.




Supplementary data files not provided
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