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Sample GSM94583 Query DataSets for GSM94583
Status Public on Feb 01, 2006
Title jiI-P7-6(1)
Sample type RNA
 
Channel 1
Source name before IFN injection
Organism Homo sapiens
Characteristics before IFN injection
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 6 hrs after IFN injection
Organism Homo sapiens
Characteristics 6 hrs after IFN injection
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Hepatitis C, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18650.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 31, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3266
Series (1)
GSE4134 Interferon alfa regulated gene expression in patients initiating interferon treatment for chronic hepatitis C

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 605 262 378 131 227 131 617 256 382 136 239 125 0 0 89 72 52 47 97 88 92 67 358 364 1.733 .577 .523 .7 .575 .542 80 440 .408 .61 110 1730 8770 47 58 31 42 0 220 110 110 .485 215 105 2.062 .44 -1.044 -1.186
2 635 171 374 140 261 31 655 161 378 150 281 21 0 0 118 53 50 51 96 31 93 9 292 302 8.419 .119 .075 .236 .217 .141 32 127 .117 .3 60 1880 8800 53 59 49 55 0 144 118 26 .1 135 18 10.019 .063 -3.325 -3.993
3 613 280 375 131 238 149 614 267 377 137 239 136 0 0 86 54 48 47 98 98 94 86 387 375 1.597 .626 .569 1.187 .665 3.549 52 299 .407 .6 90 2000 8770 48 57 59 68 0 235 110 125 .526 224 114 1.901 .478 -.927 -1.064
4 650 176 383 127 267 49 605 168 382 134 222 41 0 0 140 60 50 41 100 50 100 16 316 263 5.449 .184 .185 .216 .221 .112 12 89 .183 .5 50 2140 8790 52 57 75 80 0 148 107 41 .154 141 34 6.484 .155 -2.697 -2.688
5 662 452 375 130 287 322 674 442 377 136 299 312 0 0 90 91 53 50 100 100 98 100 609 611 .891 1.122 1.043 1.251 1.144 .616 52 274 .807 .8 90 2280 8770 48 57 87 96 0 380 109 271 .943 371 262 1.061 .877 -.085 -.19
6 401 150 376 130 25 20 392 145 377 134 16 15 0 0 86 55 52 49 28 30 15 8 45 31 1.25 .8 .938 1.234 .712 1.953 80 286 .049 .06 100 2430 8760 47 57 102 112 -50 126 109 17 .672 122 13 1.488 .788 -.573 -.344
7 714 644 372 129 342 515 715 654 373 136 343 525 0 0 107 169 50 49 97 98 97 98 857 868 .664 1.506 1.531 1.663 1.45 .951 80 275 1.286 .86 100 2540 8770 48 58 113 123 0 541 108 433 1.265 550 441 .79 1.286 .34 .363
8 539 336 366 132 173 204 542 325 368 137 176 193 0 0 69 94 49 50 95 96 91 86 377 369 .848 1.179 1.097 1.352 1.093 1.058 80 342 .791 .7 100 2690 8770 48 58 128 138 0 282 111 171 .991 273 162 1.009 .922 -.013 -.118
9 521 215 359 137 162 78 538 209 359 147 179 72 0 0 88 66 54 59 81 56 71 25 240 251 2.077 .481 .402 .636 .483 .643 32 111 .34 .48 60 2850 8780 51 57 146 152 0 181 115 66 .405 176 61 2.472 .338 -1.305 -1.565
10 597 269 366 134 231 135 589 265 368 140 223 131 0 0 82 73 55 54 98 91 93 58 366 354 1.711 .584 .587 .704 .618 .517 80 280 .414 .61 100 2960 8770 48 58 155 165 0 226 113 113 .491 223 110 2.036 .494 -1.026 -1.018
11 647 284 369 139 278 145 654 288 371 143 285 149 0 0 99 83 53 48 100 87 95 65 423 434 1.917 .522 .523 .637 .511 .55 80 276 .396 .63 100 3100 8770 48 58 169 179 0 239 117 122 .438 242 125 2.282 .439 -1.19 -1.187
12 562 292 370 135 192 157 546 282 374 139 176 147 0 0 75 74 51 48 97 97 90 78 349 323 1.223 .818 .835 .946 .737 .614 80 290 .542 .63 100 3240 8770 48 58 183 193 0 245 113 132 .687 237 124 1.455 .702 -.541 -.511
13 644 348 375 134 269 214 635 352 377 140 260 218 0 0 88 97 57 53 100 95 96 85 483 478 1.257 .796 .838 .885 .791 .505 80 293 .609 .73 100 3380 8770 48 58 197 207 0 292 113 180 .669 296 183 1.496 .705 -.581 -.505
14 682 395 372 134 310 261 675 397 370 138 303 263 0 0 114 102 52 49 98 100 97 95 571 566 1.188 .842 .868 1.049 .852 1.152 80 304 .648 .78 100 3520 8760 47 57 211 221 0 332 113 219 .708 334 221 1.413 .729 -.499 -.455
15 525 248 364 137 161 111 537 234 366 140 173 97 0 0 79 85 54 49 90 78 75 48 272 270 1.45 .689 .561 1.016 .537 1.103 52 192 .357 .44 80 3650 8740 46 54 225 233 0 208 115 93 .579 197 82 1.726 .471 -.787 -1.086
16 804 535 371 139 433 396 807 535 371 144 436 396 0 0 101 124 53 51 100 98 98 97 829 832 1.093 .915 .908 .954 .896 .369 80 365 .79 .65 110 3780 8760 46 57 236 247 0 450 117 333 .769 450 333 1.301 .763 -.38 -.39
17 775 840 376 135 399 705 772 862 377 142 396 727 0 0 114 203 51 50 100 100 100 100 1104 1123 .566 1.767 1.836 1.822 1.766 .501 80 275 1.549 .9 100 3930 8770 48 58 252 262 0 706 113 592 1.485 724 611 .673 1.543 .57 .625
18 699 287 378 138 321 149 700 292 379 143 322 154 0 0 86 73 50 49 100 91 100 72 470 476 2.154 .464 .478 .501 .462 .3 80 280 .378 .69 110 4070 8770 47 58 265 276 0 241 116 125 .39 245 129 2.564 .402 -1.358 -1.315
19 716 1039 375 135 341 904 718 1041 381 142 343 906 0 0 95 197 52 52 100 100 100 100 1245 1249 .377 2.651 2.641 2.823 2.769 .888 80 276 2.241 .9 110 4200 8770 47 58 278 289 0 873 113 760 2.228 875 761 .449 2.22 1.156 1.15
20 788 638 385 135 403 503 784 635 388 142 399 500 0 0 108 131 56 50 100 100 98 100 906 899 .801 1.248 1.253 1.347 1.269 .524 80 288 1.077 .87 110 4330 8770 47 58 291 302 0 536 113 423 1.049 534 420 .953 1.053 .069 .075

Total number of rows: 43392

Table truncated, full table size 9167 Kbytes.




Supplementary data files not provided
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