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Sample GSM475044 Query DataSets for GSM475044
Status Public on Apr 12, 2010
Title LLAT 5B
Sample type RNA
 
Channel 1
Source name Stratagene common human reference
Organism Homo sapiens
Characteristics reference: Stratagene common human reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name LLAT 5B
Organism Homo sapiens
Characteristics individual: patient5
treatment: IFNa/AZT
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4000B
Description Simple annotation: T-cell, human tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40695.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 24, 2009
Last update date Apr 12, 2010
Contact name Ash A Alizadeh
E-mail(s) arasha@stanford.edu
Organization name Stanford University School of Medicine
Department Medicine, Divisions of Hematology and of Oncology
Lab Alizadeh
Street address 269 Campus Drive, CCSR 1145c
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9716
Series (1)
GSE19160 Adult T-cell leukemia-lymphoma and AZT-IFNa combination therapy

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 294 533 91 89 203 444 216 150 93 98 125 61 0 0 294 1227 22 40 100 65 96 46 647 186 .457 2.187 .488 .615 .556 3.096 32 218 3.724 .96 70 1340 7210 69 76 50 57 -100 957 160 797 3.927 269 110 .255 .876 1.973 -.191
2 2034 144 91 86 1943 58 2077 142 94 97 1986 56 0 0 790 49 23 69 100 44 100 3 2001 2042 33.5 .03 .028 .035 .035 2.06 52 269 .025 .52 80 1500 7210 69 77 66 74 0 259 154 104 .054 255 101 18.66 .051 -4.222 -4.304
3 405 213 89 93 316 120 437 219 90 95 348 126 0 0 119 64 19 38 100 93 100 75 436 474 2.633 .38 .362 .375 .401 1.891 32 149 .363 .74 60 1640 7210 70 76 81 87 0 382 167 215 .682 393 226 1.467 .65 -.553 -.621
4 458 129 85 90 373 39 432 132 85 91 347 42 0 0 132 43 17 36 100 62 100 21 412 389 9.564 .105 .121 .135 .145 1.78 32 203 .095 .37 70 1790 7210 69 76 95 102 0 232 162 70 .188 237 75 5.327 .217 -2.413 -2.202
5 2670 540 85 94 2585 446 2885 527 90 96 2800 433 0 0 684 181 26 35 100 100 100 100 3031 3233 5.796 .173 .155 .168 .156 1.345 32 227 .17 .92 70 1930 7200 68 75 109 116 0 969 169 801 .31 946 777 3.228 .278 -1.691 -1.849
6 184 161 89 83 95 78 178 170 89 87 89 87 0 0 32 50 22 36 100 66 100 50 173 176 1.218 .821 .978 .803 .886 2.066 12 104 1.038 .51 50 2080 7220 71 76 125 130 0 289 149 140 1.474 305 156 .678 1.755 .56 .811
7 965 374 90 90 875 284 1030 390 90 95 940 300 0 0 345 159 20 37 100 93 100 87 1159 1240 3.081 .325 .319 .306 .325 1.494 32 164 .33 .91 60 2230 7210 70 76 140 146 0 671 162 510 .583 700 539 1.716 .573 -.779 -.803
8 316 180 87 90 229 90 306 180 87 97 219 90 0 0 68 61 20 40 100 78 100 53 319 309 2.544 .393 .411 .369 .382 2.008 32 164 .384 .56 60 2370 7210 70 76 154 160 0 323 162 162 .706 323 162 1.417 .738 -.503 -.439
9 579 189 85 92 494 97 573 190 91 96 488 98 0 0 112 67 39 38 100 78 100 61 591 586 5.093 .196 .201 .185 .204 1.965 52 257 .197 .62 80 2520 7190 67 75 168 176 0 339 165 174 .353 341 176 2.837 .361 -1.504 -1.472
10 1232 317 85 91 1147 226 693 298 87 97 608 207 0 0 2704 112 22 43 100 100 100 90 1373 815 5.075 .197 .34 .294 .338 1.961 52 276 .037 .39 90 2660 7210 68 77 181 190 0 569 163 406 .354 535 372 2.827 .611 -1.499 -.71
11 2928 233 87 94 2841 139 2944 218 92 96 2857 124 0 0 361 67 64 42 100 96 100 78 2980 2981 20.439 .049 .043 .045 .049 1.625 52 300 .047 .76 90 2810 7200 67 76 196 205 0 418 169 250 .088 391 223 11.385 .078 -3.509 -3.682
12 2597 2130 86 92 2511 2038 2763 2287 87 96 2677 2195 0 0 1070 841 24 40 100 98 100 98 4549 4872 1.232 .812 .82 .793 .808 1.367 80 374 .801 .99 100 2960 7200 67 77 211 221 0 3824 165 3659 1.457 4106 3941 .686 1.472 .543 .558
13 1824 1219 88 96 1736 1123 1778 1189 95 104 1690 1093 0 0 300 237 41 56 100 100 100 100 2859 2783 1.546 .647 .647 .643 .641 1.171 52 281 .651 .97 90 3100 7190 66 75 225 234 0 2188 172 2016 1.161 2135 1962 .861 1.161 .216 .215
14 458 380 90 106 368 274 452 394 94 118 362 288 0 0 124 107 35 72 100 96 100 85 642 650 1.343 .745 .796 .709 .716 1.606 80 296 .747 .85 100 3250 7200 67 77 240 250 0 682 190 492 1.337 707 517 .748 1.428 .419 .514
15 381 14322 86 104 295 14218 391 14597 100 127 305 14493 0 0 81 3746 120 146 99 100 75 100 14513 14798 .021 48.197 47.518 48.344 47.575 1.25 120 447 50.336 .95 130 3390 7200 65 78 252 265 0 25712 187 25526 86.528 26206 26019 .012 85.309 6.435 6.415
16 4993 6005 92 118 4901 5887 4766 5539 126 163 4674 5421 0 0 1246 1640 182 211 100 100 100 100 10788 10095 .833 1.201 1.16 1.193 1.195 1.12 52 240 1.206 .99 90 3540 7200 67 76 269 278 0 10781 212 10569 2.156 9944 9732 .464 2.082 1.109 1.058
17 6972 7238 100 128 6872 7110 7752 7899 123 161 7652 7771 0 0 3304 3655 147 171 100 100 100 100 13982 15423 .967 1.035 1.016 1.01 1.032 1.227 120 395 1.053 .99 120 3690 7200 66 78 283 295 0 12994 230 12765 1.857 14181 13951 .538 1.823 .893 .866
18 130 147 106 128 24 19 116 146 112 136 10 18 0 0 54 62 42 54 23 26 10 8 43 28 1.263 .792 1.8 1.328 1.448 3.773 80 290 2.292 .29 100 3820 7190 66 76 297 307 -50 264 230 34 1.421 262 32 .704 3.232 .507 1.692
19 9980 8369 107 127 9873 8242 9606 7197 118 136 9499 7070 0 0 3218 3369 68 53 100 100 100 100 18115 16569 1.198 .835 .744 .821 .813 1.22 80 302 .852 .98 100 3980 7190 66 76 313 323 0 15025 228 14797 1.499 12921 12693 .667 1.336 .584 .418
20 4573 2488 118 149 4455 2339 5013 2738 214 235 4895 2589 0 0 1953 991 802 450 100 100 90 88 6794 7484 1.905 .525 .529 .529 .523 1.19 120 403 .514 .99 120 4120 7200 66 78 326 338 0 4467 268 4199 .943 4916 4648 1.061 .95 -.085 -.075

Total number of rows: 43104

Table truncated, full table size 9715 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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