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Sample GSM94584 Query DataSets for GSM94584
Status Public on Feb 01, 2006
Title jiI-P3-3a
Sample type RNA
 
Channel 1
Source name contol
Organism Homo sapiens
Characteristics contol
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/2001-06/17670.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
1 321 218 216 109 105 109 324 215 215 110 108 106 0 0 53 55 30 33 90 93 81 78 214 214 .963 1.038 .981 1.772 1.155 3.447 80 372 .696 .67 100 2200 8400 75 85 39 49 0 251 125 125 1.193 247 122 .838 1.128 .255 .174
2 246 128 220 109 26 19 225 128 222 112 5 19 0 0 58 39 33 33 35 36 18 11 45 24 1.368 .731 3.8 4.586 1.087 13.198 80 290 .11 .14 100 2340 8390 74 84 53 63 -50 147 125 22 .84 147 22 1.191 4.368 -.252 2.127
3 330 200 220 110 110 90 327 195 223 114 107 85 0 0 36 65 35 31 98 84 82 65 200 192 1.222 .818 .794 .982 .838 .758 52 211 .482 .51 90 2460 8400 75 84 65 74 0 230 126 103 .94 224 98 1.063 .913 -.089 -.131
4 238 124 218 107 20 17 227 116 222 114 9 9 0 0 54 44 31 38 28 25 17 11 37 18 1.176 .85 1 2.09 1.222 2.424 80 288 .276 .29 100 2610 8390 74 84 80 90 -50 143 123 20 .977 133 10 1.024 1.149 -.034 .201
5 362 206 222 113 140 93 363 202 223 115 141 89 0 0 43 50 31 37 98 88 94 59 233 230 1.505 .664 .631 .779 .704 .543 52 200 .493 .59 80 2730 8400 76 84 93 101 0 237 130 107 .764 232 102 1.31 .726 -.389 -.463
6 249 124 224 111 25 13 225 122 226 111 1 11 0 0 70 46 31 32 33 32 23 7 38 12 1.923 .52 11 3.8 1.039 8.121 80 294 .294 .36 100 2890 8390 74 84 108 118 -50 143 128 15 .598 140 13 1.673 12.644 -.743 3.66
7 350 231 224 111 126 120 358 235 226 113 134 124 0 0 58 67 31 32 95 91 86 76 246 258 1.05 .952 .925 1.093 .913 .719 80 280 .731 .76 100 3000 8400 75 85 119 129 0 266 128 138 1.095 270 143 .914 1.064 .131 .089
8 311 231 226 115 85 116 307 234 226 118 81 119 0 0 33 64 32 35 92 90 76 73 201 200 .733 1.365 1.469 1.651 1.271 1.321 52 267 .74 .55 90 3140 8410 76 85 133 142 0 266 132 133 1.569 269 137 .638 1.689 .65 .756
9 337 150 224 120 113 30 334 147 230 128 110 27 0 0 42 38 34 40 100 33 83 8 143 137 3.767 .265 .245 .493 .255 .515 12 90 .19 .28 50 3280 8380 75 80 149 154 0 172 138 34 .305 169 31 3.277 .282 -1.712 -1.826
10 357 203 233 122 124 81 364 200 239 125 131 78 0 0 38 46 33 40 98 84 92 48 205 209 1.531 .653 .595 .809 .598 .7 52 267 .498 .57 90 3420 8400 75 84 161 170 0 233 140 93 .751 230 90 1.332 .684 -.413 -.547
11 337 215 229 118 108 97 346 214 231 120 117 96 0 0 118 63 30 37 76 84 73 61 205 213 1.113 .898 .821 1.074 .785 1.218 52 212 .432 .62 80 3550 8400 76 84 175 183 0 247 136 111 1.032 246 110 .969 .943 .046 -.084
12 310 199 215 114 95 85 311 199 218 117 96 85 0 0 35 55 32 35 93 81 84 53 180 181 1.118 .895 .885 1.211 .971 1.301 32 214 .401 .42 70 3690 8400 76 83 189 196 0 229 131 98 1.028 229 98 .972 1.018 .04 .025
13 331 185 216 117 115 68 347 178 217 120 131 61 0 0 131 63 34 38 76 63 63 42 183 192 1.691 .591 .466 .605 .505 .532 52 324 .374 .61 90 3860 8390 74 83 205 214 0 213 134 78 .68 205 70 1.471 .535 -.557 -.902
14 328 214 224 111 104 103 330 214 225 116 106 103 0 0 44 53 32 38 98 90 75 61 207 209 1.01 .99 .972 1.275 .939 .876 52 261 .528 .52 90 3990 8390 74 83 218 227 0 246 128 118 1.138 246 118 .878 1.117 .187 .159
15 321 205 229 117 92 88 325 205 233 125 96 88 0 0 33 61 37 42 94 73 73 50 180 184 1.045 .957 .917 1.183 1.039 1 52 274 .478 .46 90 4110 8400 75 84 230 239 0 236 134 101 1.099 236 101 .91 1.054 .137 .075
16 431 402 230 116 201 286 433 394 233 122 203 278 0 0 56 108 37 38 100 100 97 98 487 481 .703 1.423 1.369 1.466 1.354 .541 80 372 1.25 .86 100 4250 8400 75 85 244 254 0 462 133 329 1.636 453 320 .611 1.574 .71 .655
17 425 377 221 112 204 265 421 370 223 116 200 258 0 0 41 85 29 34 100 100 100 100 469 458 .77 1.299 1.29 1.344 1.205 .509 52 282 1.067 .83 90 4400 8380 73 82 259 268 0 433 129 305 1.493 425 297 .67 1.483 .578 .568
18 343 206 218 112 125 94 353 208 219 114 135 96 0 0 51 51 30 34 97 91 83 58 219 231 1.33 .752 .711 .975 .803 .784 80 306 .525 .62 100 4550 8380 73 83 274 284 0 237 129 108 .864 239 110 1.157 .817 -.21 -.291
19 317 299 216 111 101 188 324 285 218 114 108 174 0 0 46 86 31 35 91 97 78 91 289 282 .537 1.861 1.611 2.223 1.705 1.465 80 287 1.272 .74 100 4670 8390 74 84 286 296 0 344 128 216 2.14 328 200 .467 1.852 1.097 .889
20 346 238 220 114 126 124 346 241 218 118 126 127 0 0 53 60 29 37 95 91 91 76 250 253 1.016 .984 1.008 1.337 .963 1.812 80 306 .693 .7 100 4810 8390 74 84 300 310 0 274 131 143 1.131 277 146 .884 1.159 .178 .212

Total number of rows: 43392

Table truncated, full table size 9157 Kbytes.




Supplementary data files not provided
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