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Sample GSM94556 Query DataSets for GSM94556
Status Public on Feb 01, 2006
Title jiI-P5-6(2)
Sample type RNA
 
Channel 1
Source name P5-0
Organism Homo sapiens
Characteristics P5-0
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 6 hours after IFN inj
Organism Homo sapiens
Characteristics 6 hours after IFN inj
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Hepatitis C, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20996.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
1 540 260 300 112 240 148 546 262 302 113 246 150 0 0 72 74 40 41 98 92 98 81 388 396 1.622 .617 .61 .701 .642 .594 80 363 .518 .74 100 1640 8910 54 64 39 49 0 271 117 154 .642 273 156 1.557 .635 -.639 -.655
2 549 167 291 112 258 55 553 163 293 117 262 51 0 0 106 50 37 46 93 62 93 18 313 313 4.691 .213 .195 .368 .222 .623 32 124 .164 .41 70 1750 8930 57 64 51 58 0 174 117 57 .222 170 53 4.503 .203 -2.171 -2.302
3 494 273 278 112 216 161 487 278 285 117 209 166 0 0 74 69 36 44 100 96 98 81 377 375 1.342 .745 .794 .819 .658 .453 80 295 .64 .76 100 1910 8910 54 64 66 76 0 284 117 168 .776 290 173 1.288 .827 -.365 -.273
4 306 136 281 109 25 27 299 131 283 114 18 22 0 0 62 61 37 41 32 37 20 17 52 40 .926 1.08 1.222 3.315 1.205 5.758 80 237 .247 .24 100 2050 8900 53 63 80 90 -50 142 114 28 1.125 136 23 .889 1.273 .17 .348
5 556 474 278 104 278 370 553 467 278 108 275 363 0 0 87 132 36 34 100 100 100 98 648 638 .751 1.331 1.32 1.409 1.282 .6 80 249 1.19 .88 110 2170 8920 54 65 91 102 0 494 108 385 1.386 486 378 .721 1.375 .471 .459
6 325 146 289 111 36 35 304 137 293 114 15 26 0 0 81 55 44 39 27 42 18 23 71 41 1.029 .972 1.733 2.097 .907 2.809 80 261 .2 .25 100 2320 8900 53 63 107 117 -50 152 116 36 1.013 143 27 .987 1.806 .018 .852
7 673 638 317 119 356 519 697 625 318 120 380 506 0 0 126 197 45 42 97 98 97 98 875 886 .686 1.458 1.332 1.579 1.434 .744 80 243 1.299 .9 100 2440 8900 53 63 119 129 0 665 124 541 1.519 651 527 .658 1.387 .603 .472
8 505 377 318 120 187 257 501 373 320 121 183 253 0 0 72 101 43 43 98 100 90 96 444 436 .728 1.374 1.383 1.616 1.306 1.026 80 277 1.009 .76 100 2580 8910 54 64 133 143 0 393 125 268 1.432 389 264 .699 1.44 .518 .526
9 504 164 316 123 188 41 496 167 317 132 180 44 0 0 39 26 50 56 100 33 100 0 229 224 4.585 .218 .244 .262 .271 .155 12 74 .299 .53 50 2680 8910 56 61 145 150 0 171 128 43 .227 174 46 4.402 .255 -2.138 -1.974
10 529 254 307 120 222 134 537 249 311 124 230 129 0 0 76 71 43 46 98 91 93 71 356 359 1.657 .604 .561 .745 .603 .499 80 320 .47 .68 100 2840 8900 53 63 159 169 0 265 125 140 .629 259 134 1.59 .584 -.669 -.775
11 689 534 306 115 383 419 678 529 311 120 372 414 0 0 117 136 45 44 100 100 98 98 802 786 .914 1.094 1.113 1.155 1.085 .398 80 291 .987 .89 100 2980 8900 53 63 173 183 0 556 120 436 1.14 551 431 .878 1.159 .188 .213
12 521 308 296 110 225 198 523 297 300 112 227 187 0 0 69 93 39 41 98 97 96 91 423 414 1.136 .88 .824 .969 .86 .607 80 289 .733 .78 100 3130 8900 53 63 188 198 0 321 115 206 .917 309 195 1.091 .858 -.126 -.221
13 515 285 288 113 227 172 526 276 291 116 238 163 0 0 78 72 38 39 98 97 93 91 399 401 1.32 .758 .685 .865 .713 .517 80 269 .602 .74 100 3260 8900 53 63 201 211 0 297 118 179 .789 288 170 1.267 .713 -.341 -.487
14 504 308 286 110 218 198 506 308 288 115 220 198 0 0 85 90 39 42 98 98 95 91 416 418 1.101 .908 .9 1.084 .842 .82 80 302 .697 .74 100 3400 8890 52 62 215 225 0 321 115 206 .946 321 206 1.057 .938 -.08 -.093
15 404 242 278 112 126 130 399 236 284 115 121 124 0 0 61 67 38 41 92 94 82 76 256 245 .969 1.032 1.025 1.436 1.068 1.358 52 192 .572 .56 80 3550 8880 52 60 231 239 0 252 117 135 1.075 246 129 .93 1.067 .104 .094
16 592 501 276 112 316 389 591 494 282 117 315 382 0 0 91 120 40 44 100 100 98 98 705 697 .812 1.231 1.213 1.294 1.242 .442 80 273 1.139 .9 100 3670 8890 52 62 242 252 0 522 117 405 1.282 515 398 .78 1.263 .359 .337
17 561 667 282 114 279 553 569 672 283 121 287 558 0 0 105 198 43 55 98 98 95 97 832 845 .505 1.982 1.944 2.196 1.953 1.047 80 277 1.726 .9 100 3820 8890 52 62 257 267 0 695 119 576 2.065 700 581 .484 2.025 1.046 1.018
18 498 255 284 115 214 140 498 254 332 140 214 139 0 0 65 80 361 170 1 36 0 1 354 353 1.529 .654 .65 .764 .616 .65 52 240 .406 .89 90 3960 8880 51 60 271 280 0 266 120 146 .681 265 145 1.467 .677 -.553 -.564
19 468 971 280 110 188 861 472 966 321 129 192 856 0 0 52 187 324 149 1 100 0 100 1049 1048 .218 4.58 4.458 4.876 4.594 1.569 80 300 .612 .5 110 4100 8890 51 62 284 295 0 1011 115 897 4.771 1006 892 .21 4.644 2.254 2.215
20 470 371 277 115 193 256 466 379 282 122 189 264 0 0 58 98 41 45 100 100 98 96 449 453 .754 1.326 1.397 1.441 1.364 .688 80 238 1.108 .79 100 4230 8890 52 62 298 308 0 386 120 267 1.382 395 275 .724 1.455 .466 .541

Total number of rows: 43392

Table truncated, full table size 9171 Kbytes.




Supplementary data files not provided
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