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Sample GSM94557 Query DataSets for GSM94557
Status Public on Feb 01, 2006
Title jiI-P5-3a
Sample type RNA
 
Channel 1
Source name P5-3c
Organism Homo sapiens
Characteristics P5-3c
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name P5-3a
Organism Homo sapiens
Characteristics P5-3a
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Hepatitis C, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/20998.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
1 360 243 236 104 124 139 359 235 244 110 123 131 0 0 48 70 56 44 92 92 60 75 263 254 .892 1.121 1.065 1.329 1.032 1.04 80 383 .779 .65 100 1940 8530 56 66 53 63 0 187 80 107 .862 181 101 1.16 .819 -.214 -.288
2 393 144 233 102 160 42 393 132 231 110 160 30 0 0 51 53 29 40 100 40 100 25 202 190 3.81 .263 .188 .45 .333 .385 32 158 .133 .23 70 2070 8550 59 66 67 74 0 111 78 32 .202 102 23 4.952 .144 -2.308 -2.794
3 339 248 222 105 117 143 338 238 223 112 116 133 0 0 43 80 31 42 98 90 88 78 260 249 .818 1.222 1.147 1.358 1.202 .812 80 303 .876 .68 100 2210 8540 57 67 80 90 0 191 81 110 .94 183 102 1.064 .882 -.089 -.181
4 245 119 226 102 19 17 240 119 228 108 14 17 0 0 42 46 30 39 28 30 15 8 36 31 1.118 .895 1.214 3.433 1.281 6.764 80 257 .261 .23 100 2360 8530 56 66 95 105 -50 92 78 13 .688 92 13 1.453 .934 -.539 -.098
5 352 291 221 102 131 189 348 286 224 110 127 184 0 0 41 78 31 42 100 98 95 93 320 311 .693 1.443 1.449 1.606 1.362 .907 80 236 1.096 .73 100 2480 8540 57 67 107 117 0 224 78 145 1.11 220 142 .901 1.114 .15 .156
6 240 118 210 99 30 19 231 115 201 103 21 16 0 0 45 43 52 38 26 27 5 11 49 37 1.579 .633 .762 3.191 .923 8.173 80 285 .244 .25 100 2630 8530 56 66 122 132 -50 91 76 15 .487 88 12 2.053 .586 -1.037 -.771
7 446 557 190 97 256 460 439 569 178 103 249 472 0 0 49 117 72 42 100 100 100 100 716 721 .557 1.797 1.896 1.841 1.83 .502 52 244 1.423 .88 90 2740 8530 56 65 133 142 0 428 75 354 1.382 438 363 .723 1.458 .467 .544
8 321 429 213 106 108 323 320 427 233 113 107 321 0 0 34 103 127 45 34 100 0 100 431 428 .334 2.991 3 3.356 2.961 1.668 52 264 2.028 .78 90 2890 8530 56 65 148 157 0 330 82 248 2.301 328 247 .435 2.308 1.202 1.206
9 326 182 222 127 104 55 337 198 222 124 115 71 0 0 42 61 28 44 91 58 91 33 159 186 1.891 .529 .617 .861 .609 .586 12 79 .302 .38 50 2990 8540 59 64 160 165 0 140 98 42 .407 152 55 2.458 .475 -1.298 -1.074
10 365 249 232 117 133 132 367 241 231 124 135 124 0 0 44 78 32 48 100 86 92 66 265 259 1.008 .992 .919 1.079 .918 .683 80 375 .807 .71 100 3160 8530 56 66 175 185 0 192 90 102 .763 185 95 1.31 .707 -.389 -.501
11 396 285 236 112 160 173 400 279 237 117 164 167 0 0 65 93 32 45 95 90 91 82 333 331 .925 1.081 1.018 1.343 1.051 1.205 80 286 .874 .75 100 3290 8530 56 66 188 198 0 219 86 133 .832 215 128 1.202 .783 -.266 -.352
12 367 301 243 111 124 190 373 288 245 115 130 177 0 0 51 96 31 41 95 97 86 91 314 307 .653 1.532 1.362 1.962 1.639 1.575 80 279 1.097 .71 100 3440 8540 57 67 203 213 0 232 85 146 1.179 222 136 .848 1.047 .237 .067
13 409 281 250 112 159 169 407 276 248 116 157 164 0 0 55 74 31 40 98 100 96 86 328 321 .941 1.063 1.045 1.277 1.045 1.015 80 297 .813 .73 100 3590 8530 56 66 218 228 0 216 86 130 .818 212 126 1.223 .804 -.291 -.316
14 394 302 230 109 164 193 402 299 232 112 172 190 0 0 62 70 31 40 98 97 96 93 357 362 .85 1.177 1.105 1.323 1.161 .694 80 375 .934 .78 110 3720 8520 54 65 230 241 0 232 84 148 .905 230 146 1.105 .85 -.144 -.235
15 308 204 223 110 85 94 307 208 223 115 84 98 0 0 41 53 30 41 90 84 71 59 179 182 .904 1.106 1.167 1.523 1.035 1.592 32 150 .474 .42 70 3860 8520 56 63 246 253 0 157 85 72 .851 160 75 1.176 .897 -.233 -.156
16 388 457 221 112 167 345 385 466 224 115 164 354 0 0 52 108 31 41 100 100 96 100 512 518 .484 2.066 2.159 2.291 2.141 1.077 80 282 1.725 .85 100 3980 8530 56 66 257 267 0 352 86 265 1.589 358 272 .629 1.66 .668 .732
17 382 441 231 111 151 330 382 443 230 115 151 332 0 0 60 143 37 43 95 100 91 97 481 483 .458 2.185 2.199 2.471 2.145 1.257 80 279 1.757 .83 100 4130 8520 55 65 272 282 0 339 85 254 1.681 341 255 .595 1.691 .749 .758
18 358 224 236 111 122 113 359 218 239 116 123 107 0 0 46 70 35 44 97 85 88 63 235 230 1.08 .926 .87 1.135 1.009 .856 80 270 .672 .61 100 4270 8520 55 65 286 296 0 172 85 87 .712 168 82 1.404 .669 -.489 -.58
19 325 451 237 113 88 338 328 457 239 113 91 344 0 0 45 110 29 39 91 100 73 100 426 435 .26 3.841 3.78 6.423 3.561 9.234 80 288 2.188 .7 110 4400 8530 55 66 298 309 0 347 87 260 2.955 352 265 .338 2.908 1.563 1.54
20 386 407 235 106 151 301 380 405 237 111 145 299 0 0 43 91 32 40 100 100 97 98 452 444 .502 1.993 2.062 2.113 2.072 .778 80 251 1.705 .84 100 4530 8530 56 66 312 322 0 313 82 232 1.533 312 230 .652 1.586 .617 .666

Total number of rows: 43392

Table truncated, full table size 9084 Kbytes.




Supplementary data files not provided
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