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Sample GSM94558 Query DataSets for GSM94558
Status Public on Feb 01, 2006
Title z2004-W-NR-P5IFNa6h(duplicated case)
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 5 hrs after IFN treatment
Organism Homo sapiens
Characteristics 5 hrs after IFN treatment
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Hepatitis C, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17664.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
1 348 168 236 124 112 44 348 168 236 131 112 44 0 0 37 44 29 38 98 51 92 23 156 156 2.545 .393 .393 .55 .481 .466 52 292 .236 .31 90 2230 8610 72 81 42 51 0 79 58 21 .184 79 21 5.422 .184 -2.439 -2.439
2 266 149 236 128 30 21 247 145 238 133 11 17 0 0 73 44 29 38 33 31 23 8 51 28 1.429 .7 1.545 2.265 .786 6.015 80 318 .251 .29 100 2380 8590 70 80 57 67 -50 70 60 10 .329 68 8 3.043 .726 -1.605 -.463
3 353 194 241 129 112 65 359 178 241 134 118 49 0 0 44 57 28 40 96 63 86 36 177 167 1.723 .58 .415 .822 .565 1.215 52 201 .392 .44 90 2500 8610 72 81 69 78 0 91 61 31 .272 84 23 3.67 .195 -1.876 -2.359
4 252 143 235 129 17 14 247 136 238 133 12 7 0 0 41 48 30 39 33 26 13 10 31 19 1.214 .824 .583 3.057 1.057 7.181 80 300 .307 .24 100 2650 8590 70 80 84 94 -50 67 61 7 .387 64 3 2.586 .274 -1.371 -1.868
5 398 255 239 128 159 127 388 253 240 134 149 125 0 0 54 51 31 38 100 98 98 86 286 274 1.252 .799 .839 .943 .767 .614 52 191 .531 .63 90 2770 8610 72 81 96 105 0 120 60 60 .375 119 59 2.667 .394 -1.415 -1.344
6 276 149 239 132 37 17 257 144 241 137 18 12 0 0 71 53 31 40 38 26 26 12 54 30 2.176 .459 .667 2.681 .741 8.848 80 289 .271 .31 100 2920 8590 70 80 111 121 -50 70 62 8 .216 68 6 4.636 .313 -2.213 -1.676
7 397 375 244 142 153 233 398 375 245 144 154 233 0 0 50 75 31 39 98 100 96 100 386 387 .657 1.523 1.513 1.784 1.403 1.374 52 198 1.212 .82 90 3040 8600 71 80 123 132 0 176 67 109 .715 176 109 1.399 .71 -.484 -.493
8 334 285 244 140 90 145 335 292 247 143 91 152 0 0 46 70 31 38 86 95 75 83 235 243 .621 1.611 1.67 2.739 1.471 5.878 80 343 .976 .65 100 3180 8600 71 81 137 147 0 134 66 68 .756 137 71 1.322 .784 -.403 -.351
9 384 200 246 138 138 62 381 203 250 139 135 65 0 0 74 62 32 37 93 71 87 46 200 200 2.226 .449 .481 .697 .556 .529 32 154 .303 .46 70 3330 8610 73 80 153 160 0 94 65 29 .211 95 31 4.741 .226 -2.245 -2.145
10 367 194 246 136 121 58 362 192 249 137 116 56 0 0 52 46 31 38 93 68 88 35 179 172 2.086 .479 .483 .942 .545 1.73 80 288 .327 .46 100 3450 8600 71 81 164 174 0 91 64 27 .225 90 26 4.444 .227 -2.152 -2.141
11 368 246 244 139 124 107 379 243 245 140 135 104 0 0 53 70 32 39 92 86 87 67 231 239 1.159 .863 .77 1.079 .853 .8 80 262 .609 .62 100 3590 8600 71 81 178 188 0 115 65 50 .405 114 49 2.468 .362 -1.304 -1.467
12 355 204 244 145 111 59 356 196 248 145 112 51 0 0 57 53 35 39 87 63 77 30 170 163 1.881 .532 .455 1.023 .628 1.843 80 325 .319 .41 100 3730 8600 71 81 192 202 0 96 68 28 .25 92 24 4.007 .214 -2.003 -2.226
13 361 200 245 139 116 61 364 201 248 141 119 62 0 0 51 55 48 40 91 66 63 38 177 181 1.902 .526 .521 .716 .565 .568 80 298 .353 .46 100 3890 8590 70 80 208 218 0 94 65 29 .247 94 29 4.05 .245 -2.018 -2.031
14 356 220 246 141 110 79 359 215 247 148 113 74 0 0 45 63 33 57 96 62 82 26 189 187 1.392 .718 .655 .877 .79 .606 80 245 .519 .57 100 4020 8590 70 80 221 231 0 103 66 37 .337 101 35 2.966 .307 -1.568 -1.702
15 340 205 250 140 90 65 337 194 250 145 87 54 0 0 50 47 34 41 87 66 68 32 155 141 1.385 .722 .621 .907 .663 .875 80 245 .407 .44 100 4140 8600 71 81 233 243 0 96 66 31 .339 91 25 2.949 .291 -1.56 -1.779
16 407 291 247 140 160 151 410 294 248 142 163 154 0 0 58 77 31 41 97 93 97 78 311 317 1.06 .944 .945 1.055 .937 .679 80 331 .734 .71 110 4270 8600 70 81 245 256 0 137 66 71 .443 138 72 2.257 .444 -1.174 -1.173
17 371 616 244 139 127 477 364 638 244 140 120 499 0 0 51 160 31 39 98 100 87 100 604 619 .266 3.756 4.158 4.308 3.928 1.964 80 320 2.738 .81 100 4430 8580 69 79 262 272 0 289 65 224 1.763 300 234 .567 1.952 .818 .965
18 360 196 241 143 119 53 358 186 242 144 117 43 0 0 47 50 33 38 98 55 88 28 172 160 2.245 .445 .368 .601 .4 .524 80 292 .324 .44 100 4560 8580 69 79 275 285 0 92 67 25 .209 87 20 4.782 .173 -2.258 -2.535
19 364 432 241 142 123 290 358 439 241 143 117 297 0 0 50 87 33 39 97 100 93 100 413 414 .424 2.358 2.538 2.752 2.211 1.884 80 285 1.617 .8 100 4690 8590 70 80 288 298 0 203 67 136 1.107 206 139 .903 1.192 .147 .253
20 377 300 239 142 138 158 380 294 240 143 141 152 0 0 44 55 31 38 98 100 94 92 296 293 .873 1.145 1.078 1.33 1.163 .793 52 242 .818 .74 90 4820 8580 69 78 301 310 0 141 67 74 .538 138 71 1.86 .506 -.896 -.982

Total number of rows: 43392

Table truncated, full table size 9010 Kbytes.




Supplementary data files not provided
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