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Sample GSM71836 Query DataSets for GSM71836
Status Public on Aug 25, 2005
Title RV72 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 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/2002-08/31845.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
1 128 334 59 195 69 139 117 303 60 205 58 108 0 0 64 139 9 57 74 62 63 46 208 166 .496 2.014 1.862 1 1 1 120 529 1 .87 130 1910 9270 52 65 24 37 0 402 235 167 2.427 365 130 .412 2.243 1.279 1.166
2 253 562 58 192 195 370 268 566 59 199 210 374 0 0 146 299 9 57 91 75 80 67 565 584 .527 1.897 1.781 1 1 1 120 337 1 .94 130 2050 9270 52 65 38 51 0 677 231 446 2.286 682 451 .437 2.146 1.193 1.101
3 150 367 57 194 93 173 108 279 58 197 51 85 0 0 98 197 8 41 75 64 65 50 266 136 .538 1.86 1.667 1 1 1 120 356 1 .91 130 2200 9260 51 64 53 66 0 442 234 208 2.241 336 102 .446 2.008 1.164 1.006
4 127 382 56 194 71 188 126 329 56 199 70 135 0 0 56 178 7 46 87 72 79 57 259 205 .378 2.648 1.929 1 1 1 120 365 1 .83 130 2340 9260 51 64 67 80 0 460 234 227 3.19 396 163 .313 2.324 1.674 1.216
5 250 513 56 199 194 314 195 424 57 205 139 225 0 0 181 282 9 54 86 77 77 66 508 364 .618 1.619 1.619 1 1 1 80 237 1 .93 100 2490 9260 53 63 84 94 0 618 240 378 1.95 511 271 .513 1.95 .964 .964
6 94 417 54 198 40 219 76 322 55 203 22 124 0 0 43 232 9 46 72 72 57 57 259 146 .183 5.475 5.636 1 1 1 120 376 1 .79 130 2640 9260 51 64 97 110 0 502 239 264 6.596 388 149 .152 6.791 2.722 2.764
7 365 1289 54 196 311 1093 286 1142 54 203 232 946 0 0 283 958 7 43 94 86 88 80 1404 1178 .285 3.514 4.078 1 1 1 120 357 1 .97 130 2800 9260 51 64 113 126 0 1553 236 1317 4.234 1376 1140 .236 4.913 2.082 2.297
8 304 511 54 205 250 306 258 465 55 208 204 260 0 0 215 459 8 42 93 81 90 70 556 464 .817 1.224 1.275 1 1 1 120 342 1 .63 130 2940 9260 51 64 127 140 0 616 247 369 1.475 560 313 .678 1.536 .56 .619
9 177 431 54 208 123 223 180 429 55 211 126 221 0 0 90 164 8 38 87 85 81 77 346 347 .552 1.813 1.754 1 1 1 120 363 1 .86 130 3090 9250 50 63 142 155 0 519 251 269 2.184 517 266 .458 2.113 1.127 1.079
10 93 446 54 206 39 240 89 444 56 212 35 238 0 0 34 195 8 36 80 84 68 75 279 273 .163 6.154 6.8 1 1 1 120 350 1 .85 130 3240 9250 50 63 157 170 0 537 248 289 7.414 535 287 .135 8.193 2.89 3.034
11 3151 604 55 218 3096 386 3727 633 57 225 3672 415 0 0 1757 226 16 71 99 90 98 81 3482 4087 8.021 .125 .113 1 1 1 120 345 1 .92 130 3380 9250 50 63 171 184 0 728 263 465 .15 763 500 6.657 .136 -2.735 -2.877
12 815 646 57 227 758 419 693 575 58 239 636 348 0 0 695 332 16 73 90 83 80 70 1177 984 1.809 .553 .547 1 1 1 120 341 1 .92 130 3530 9250 50 63 186 199 0 778 273 505 .666 693 419 1.502 .659 -.586 -.601
13 386 496 56 229 330 267 410 493 58 240 354 264 0 0 214 190 17 74 91 80 87 66 597 618 1.236 .809 .746 1 1 1 120 324 1 .9 130 3670 9250 50 63 200 213 0 598 276 322 .975 594 318 1.026 .899 -.037 -.154
14 173 422 54 210 119 212 171 456 55 215 117 246 0 0 84 161 7 42 88 77 84 69 331 363 .561 1.782 2.103 1 1 1 120 369 1 .85 130 3810 9230 48 61 214 227 0 508 253 255 2.146 549 296 .466 2.533 1.102 1.341
15 73 333 53 199 20 134 72 311 53 203 19 112 0 0 19 143 7 36 81 77 59 65 154 131 .149 6.7 5.895 1 1 1 120 342 1 .8 130 3960 9240 49 62 229 242 0 401 240 161 8.072 375 135 .124 7.102 3.013 2.828
16 515 697 52 190 463 507 488 684 53 196 436 494 0 0 324 402 8 44 94 85 91 80 970 930 .913 1.095 1.133 1 1 1 120 336 1 .87 130 4100 9240 49 62 243 256 0 840 229 611 1.319 824 595 .758 1.365 .4 .449
17 981 779 52 182 929 597 1059 816 56 213 1007 634 0 0 497 373 29 264 92 76 90 62 1526 1641 1.556 .643 .63 1 1 1 120 371 1 .8 130 4250 9230 48 61 258 271 0 939 219 719 .774 983 764 1.292 .759 -.369 -.399
18 76 331 52 187 24 144 70 282 55 213 18 95 0 0 27 181 30 273 30 15 8 5 168 113 .167 6 5.278 1 1 1 120 341 1 .8 130 4400 9240 49 62 273 286 0 399 225 173 7.229 340 114 .138 6.359 2.854 2.669
19 1492 1533 52 187 1440 1346 1593 1679 53 189 1541 1492 0 0 948 922 8 37 97 92 94 86 2786 3033 1.07 .935 .968 1 1 1 120 358 1 .97 130 4540 9230 48 61 287 300 0 1847 225 1622 1.126 2023 1798 .888 1.167 .171 .222
20 525 799 51 182 474 617 573 872 53 184 522 690 0 0 217 320 8 34 95 96 92 91 1091 1212 .768 1.302 1.322 1 1 1 120 350 1 .93 130 4690 9230 48 61 302 315 0 963 219 743 1.568 1051 831 .638 1.593 .649 .671

Total number of rows: 43008

Table truncated, full table size 8779 Kbytes.




Supplementary data files not provided
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