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Sample GSM475049 Query DataSets for GSM475049
Status Public on Apr 12, 2010
Title LLAT 3B
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 3B
Organism Homo sapiens
Characteristics individual: patient3
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/2003-04/40072.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
1 196 277 74 85 122 192 193 264 76 89 119 179 0 0 38 48 15 24 100 100 100 100 314 298 .635 1.574 1.504 1.606 1.602 1.43 32 218 1.664 .85 70 2130 6980 62 69 57 64 0 478 147 331 2.717 456 309 .368 2.596 1.442 1.377
2 3206 303 79 90 3127 213 3436 289 85 90 3357 199 0 0 886 70 30 23 100 100 100 100 3340 3556 14.681 .068 .059 .067 .068 1.433 32 216 .066 .9 70 2280 6970 61 68 72 79 0 523 155 368 .118 499 344 8.505 .102 -3.088 -3.289
3 511 366 73 89 438 277 521 371 74 89 448 282 0 0 116 65 14 23 100 100 100 100 715 730 1.581 .632 .629 .638 .627 1.365 32 170 .606 .92 60 2430 6970 62 68 88 94 0 632 154 478 1.092 640 487 .916 1.087 .127 .12
4 656 255 72 91 584 164 678 259 71 90 606 168 0 0 175 67 12 22 100 96 100 93 748 774 3.561 .281 .277 .257 .25 1.696 32 158 .277 .89 60 2570 6970 62 68 102 108 0 440 157 283 .485 447 290 2.063 .479 -1.045 -1.063
5 1726 683 73 89 1653 594 1686 805 74 91 1613 716 0 0 1077 298 13 23 100 98 100 98 2247 2329 2.783 .359 .444 .47 .343 2.551 52 276 .318 .95 80 2720 6970 61 69 116 124 0 1179 154 1025 .62 1390 1236 1.612 .766 -.689 -.384
6 218 304 70 87 148 217 213 298 71 89 143 211 0 0 60 63 12 23 100 100 100 100 365 354 .682 1.466 1.476 1.548 1.5 1.64 32 214 1.595 .82 70 2870 6970 61 68 131 138 0 525 150 375 2.531 514 364 .395 2.547 1.34 1.349
7 960 762 70 89 890 673 1016 766 70 90 946 677 0 0 318 224 12 23 100 100 100 100 1563 1623 1.322 .756 .716 .772 .746 1.307 32 208 .726 .95 70 3010 6980 62 69 145 152 0 1315 154 1162 1.305 1322 1169 .766 1.235 .384 .305
8 244 263 72 89 172 174 253 262 72 90 181 173 0 0 58 46 14 24 100 100 100 100 346 354 .989 1.012 .956 1.046 .98 1.505 32 215 1.051 .85 70 3150 6970 61 68 159 166 0 454 154 300 1.746 452 299 .573 1.65 .804 .722
9 478 297 72 90 406 207 489 294 73 93 417 204 0 0 69 53 14 25 100 100 100 100 613 621 1.961 .51 .489 .501 .517 1.354 52 329 .51 .88 90 3300 6960 59 68 173 182 0 513 155 357 .88 507 352 1.136 .844 -.184 -.244
10 469 366 71 89 398 277 477 378 72 89 406 289 0 0 93 59 13 22 100 100 100 100 675 695 1.437 .696 .712 .703 .715 1.342 52 230 .693 .92 80 3450 6970 61 69 189 197 0 632 154 478 1.201 652 499 .832 1.229 .265 .297
11 1931 389 73 96 1858 293 1951 388 74 97 1878 292 0 0 277 65 13 24 100 100 100 100 2151 2170 6.341 .158 .155 .155 .162 1.307 52 294 .154 .91 90 3590 6960 59 68 202 211 0 671 166 506 .272 670 504 3.674 .268 -1.877 -1.898
12 3384 3818 77 108 3307 3710 4091 4370 79 110 4014 4262 0 0 1572 1200 15 28 100 100 100 100 7017 8276 .891 1.122 1.062 1.308 1.078 1.716 80 353 1.043 .97 100 3740 6970 60 70 217 227 0 6590 186 6404 1.937 7543 7357 .516 1.833 .953 .874
13 1326 1575 81 117 1245 1458 1344 1650 84 126 1263 1533 0 0 602 282 21 52 100 100 100 100 2703 2796 .854 1.171 1.214 1.285 1.16 1.541 80 320 1.031 .89 100 3890 6970 60 70 232 242 0 2719 202 2517 2.021 2848 2646 .495 2.095 1.015 1.067
14 420 654 81 120 339 534 427 664 82 122 346 544 0 0 104 121 16 31 100 100 100 100 873 890 .635 1.575 1.572 1.635 1.539 1.401 80 301 1.559 .93 100 4040 6970 60 70 247 257 0 1129 207 922 2.719 1146 939 .368 2.714 1.443 1.44
15 340 4730 80 128 260 4602 349 4908 83 130 269 4780 0 0 74 913 15 39 98 100 98 100 4862 5049 .056 17.7 17.77 18.101 17.424 1.27 120 456 17.704 .96 130 4180 6970 58 71 259 272 0 8165 221 7944 30.553 8472 8251 .033 30.673 4.933 4.939
16 3875 6592 83 136 3792 6456 4403 7156 85 140 4320 7020 0 0 1922 2611 15 50 100 100 100 100 10248 11340 .587 1.703 1.625 1.926 1.646 1.557 80 262 1.64 .96 100 4320 6970 60 70 275 285 0 11379 235 11144 2.939 12352 12118 .34 2.805 1.555 1.488
17 2948 8270 85 141 2863 8129 3243 8504 86 146 3158 8363 0 0 1137 3216 16 38 100 100 100 100 10992 11521 .352 2.839 2.648 2.851 2.817 1.198 120 410 2.852 .99 130 4470 6970 58 71 288 301 0 14275 243 14032 4.901 14679 14436 .204 4.571 2.293 2.193
18 106 144 86 141 20 3 93 136 86 147 7 -5 0 0 45 46 17 37 37 17 20 7 23 2 6.667 .15 null 1.574 1.85 3.475 80 252 2.531 .33 100 4610 6960 59 69 304 314 -50 249 243 5 .259 235 -9 3.862 null -1.949 null
19 5096 2625 86 146 5010 2479 5488 2751 87 150 5402 2605 0 0 2096 1037 17 38 100 100 100 100 7489 8007 2.021 .495 .482 .499 .489 1.292 120 358 .487 .98 120 4760 6960 58 70 318 330 0 4531 252 4279 .854 4749 4497 1.171 .832 -.227 -.265
20 2533 1628 88 151 2445 1477 2879 1762 89 154 2791 1611 0 0 898 529 16 37 100 100 100 100 3922 4402 1.655 .604 .577 .611 .582 1.275 120 366 .584 .97 120 4910 6960 58 70 333 345 0 2810 261 2550 1.043 3042 2781 .959 .996 .06 -.005

Total number of rows: 43104

Table truncated, full table size 9548 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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