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Sample GSM94566 Query DataSets for GSM94566
Status Public on Feb 01, 2006
Title jiI-P6-3a(2)
Sample type RNA
 
Channel 1
Source name no IFN
Organism Homo sapiens
Characteristics no IFN
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 3 hrs after IFN treatment
Organism Homo sapiens
Characteristics 3 hrs after IFN treatment
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Hepatitis C, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18772.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
1 542 181 359 139 183 42 535 175 360 146 176 36 0 0 76 55 50 55 97 40 87 15 225 212 4.357 .23 .205 .407 .318 .388 80 387 .164 .29 100 1820 8380 49 59 33 43 0 292 224 68 .37 282 58 2.701 .33 -1.434 -1.6
2 618 159 357 125 261 34 595 154 361 131 238 29 0 0 106 56 50 49 100 34 96 15 295 267 7.676 .13 .122 .282 .17 .254 32 126 .015 .04 60 1970 8400 53 59 50 56 0 256 202 55 .21 248 47 4.759 .197 -2.251 -2.347
3 596 221 361 136 235 85 598 228 361 140 237 92 0 0 83 66 50 48 98 72 93 48 320 329 2.765 .362 .388 .499 .376 .719 80 335 .268 .47 100 2100 8370 48 58 61 71 0 356 219 137 .583 368 148 1.714 .626 -.777 -.676
4 609 175 340 141 269 34 613 177 341 144 273 36 0 0 124 59 46 49 100 40 90 18 303 309 7.912 .126 .132 .383 .262 .403 32 116 .112 .29 60 2220 8390 52 58 75 81 0 282 227 55 .204 285 58 4.905 .213 -2.294 -2.233
5 775 406 333 142 442 264 758 380 336 145 425 238 0 0 85 100 53 47 100 100 100 98 706 663 1.674 .597 .56 .604 .571 .219 52 296 .539 .84 90 2370 8370 48 57 88 97 0 655 229 426 .963 613 384 1.038 .903 -.054 -.147
6 343 147 331 143 12 4 337 142 331 146 6 -1 0 0 69 45 48 49 27 11 12 3 16 5 3 .333 null .827 .333 1.189 80 319 .02 .03 100 2530 8370 48 58 104 114 -50 237 231 6 .538 229 null 1.86 null -.895 null
7 949 428 321 137 628 291 994 432 323 142 673 295 0 0 187 119 44 47 100 98 100 93 919 968 2.158 .463 .438 .483 .486 .192 80 298 .43 .87 110 2650 8380 48 59 115 126 0 690 221 469 .747 697 476 1.338 .707 -.42 -.5
8 527 499 316 140 211 359 525 498 319 146 209 358 0 0 85 98 46 47 98 100 92 100 570 567 .588 1.701 1.713 1.999 1.696 1.111 52 250 1.296 .8 90 2780 8370 48 57 129 138 0 805 226 579 2.744 803 577 .364 2.763 1.456 1.466
9 483 180 327 136 156 44 491 171 329 142 164 35 0 0 82 59 51 49 84 46 81 15 200 199 3.545 .282 .213 .451 .339 .403 32 173 .174 .27 70 2910 8360 48 55 143 150 0 290 219 71 .455 276 56 2.198 .344 -1.136 -1.539
10 542 222 327 133 215 89 537 220 328 139 210 87 0 0 81 72 47 47 98 68 93 46 304 297 2.416 .414 .414 .521 .383 .379 80 339 .287 .49 110 3050 8370 47 58 155 166 0 358 215 144 .668 355 140 1.498 .668 -.583 -.582
11 633 287 329 138 304 149 641 279 331 143 312 141 0 0 88 72 45 46 100 97 100 72 453 453 2.04 .49 .452 .527 .462 .281 80 277 .425 .77 100 3200 8370 48 58 171 181 0 463 223 240 .791 450 227 1.265 .729 -.339 -.456
12 532 216 327 142 205 74 527 208 333 148 200 66 0 0 80 61 48 49 98 62 90 33 279 266 2.77 .361 .33 .441 .363 .284 80 311 .274 .49 100 3330 8370 48 58 184 194 0 348 229 119 .582 335 106 1.718 .532 -.78 -.91
13 692 314 327 143 365 171 667 304 333 147 340 161 0 0 92 108 48 51 100 88 100 78 536 501 2.135 .468 .474 .49 .459 .26 52 266 .405 .68 90 3470 8360 47 56 198 207 0 506 231 276 .756 490 260 1.323 .764 -.404 -.389
14 689 295 348 148 341 147 678 292 359 152 330 144 0 0 109 87 64 52 100 83 100 68 488 474 2.32 .431 .436 .479 .463 .265 80 415 .353 .66 110 3620 8360 46 57 212 223 0 476 239 237 .695 471 232 1.438 .704 -.524 -.507
15 560 196 367 147 193 49 550 180 367 155 183 33 0 0 60 55 52 53 100 40 94 15 242 216 3.939 .254 .18 .406 .293 .427 52 243 .155 .25 90 3750 8350 46 55 226 235 0 316 237 79 .409 290 53 2.442 .291 -1.288 -1.782
16 936 673 366 143 570 530 931 657 367 153 565 514 0 0 127 158 54 55 100 100 100 100 1100 1079 1.075 .93 .91 .96 .921 .307 80 333 .851 .9 110 3890 8370 47 58 239 250 0 1085 231 855 1.5 1060 829 .667 1.467 .585 .553
17 1003 963 369 154 634 809 990 993 370 157 621 839 0 0 134 254 51 53 100 100 100 100 1443 1460 .784 1.276 1.351 1.284 1.28 .375 80 266 1.242 .93 100 4030 8370 48 58 254 264 0 1553 248 1305 2.058 1602 1353 .486 2.179 1.041 1.124
18 762 231 376 166 386 65 761 223 379 168 385 57 0 0 116 71 51 55 100 53 100 18 451 442 5.938 .168 .148 .224 .192 .158 80 270 .143 .41 100 4170 8370 48 58 268 278 0 373 268 105 .272 360 92 3.682 .239 -1.88 -2.066
19 750 743 369 158 381 585 758 744 371 168 389 586 0 0 155 181 52 61 98 100 97 100 966 975 .651 1.535 1.506 1.842 1.613 1.269 80 262 1.256 .86 100 4310 8370 48 58 282 292 0 1198 255 944 2.477 1200 945 .404 2.43 1.308 1.281
20 860 680 369 154 491 526 858 684 370 162 489 530 0 0 108 152 48 57 100 100 100 100 1017 1019 .933 1.071 1.084 1.107 1.046 .368 80 295 .991 .89 110 4440 8370 47 58 294 305 0 1097 248 848 1.728 1103 855 .579 1.748 .789 .806

Total number of rows: 43392

Table truncated, full table size 9195 Kbytes.




Supplementary data files not provided
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