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Sample GSM475050 Query DataSets for GSM475050
Status Public on Apr 12, 2010
Title LLAT 2B
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 2B
Organism Homo sapiens
Characteristics individual: patient2
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/2003-04/40071.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
1 162 215 94 129 68 86 164 200 97 130 70 71 0 0 35 58 21 42 88 78 75 44 154 141 .791 1.265 1.014 1.219 1.138 2.302 52 266 2.063 .57 80 2120 7550 59 67 48 56 0 407 244 163 2.394 379 134 .418 1.92 1.259 .941
2 3789 270 101 127 3688 143 3652 258 106 129 3551 131 0 0 1199 65 32 40 100 100 100 84 3831 3682 25.79 .039 .037 .038 .038 1.703 32 219 .033 .7 70 2270 7540 58 65 63 70 0 511 240 271 .073 488 248 13.627 .07 -3.768 -3.84
3 504 329 93 129 411 200 530 304 92 128 437 175 0 0 130 85 15 33 100 100 100 100 611 612 2.055 .487 .4 .468 .533 1.602 32 170 .469 .83 60 2420 7540 59 65 79 85 0 623 244 379 .921 575 331 1.086 .758 -.119 -.4
4 722 209 90 123 632 86 760 218 93 125 670 95 0 0 198 53 20 39 100 81 100 65 718 765 7.349 .136 .142 .126 .138 2.05 32 212 .138 .66 70 2560 7540 58 65 92 99 0 396 233 163 .258 413 180 3.883 .268 -1.957 -1.898
5 2618 854 93 121 2525 733 2684 868 94 127 2591 747 0 0 658 154 20 40 100 100 100 100 3258 3338 3.445 .29 .288 .293 .294 1.268 32 227 .272 .95 70 2710 7540 58 65 107 114 0 1616 229 1387 .549 1643 1414 1.82 .546 -.864 -.874
6 221 287 91 132 130 155 216 292 91 133 125 160 0 0 56 87 14 42 100 90 100 81 285 285 .839 1.192 1.28 1.127 1.284 1.891 32 164 1.634 .75 60 2850 7540 59 65 122 128 0 543 250 293 2.257 553 303 .443 2.423 1.174 1.277
7 1029 880 95 133 934 747 1117 909 94 136 1022 776 0 0 396 253 15 39 100 100 100 96 1681 1798 1.25 .8 .759 .859 .749 1.374 32 170 .764 .96 60 3000 7540 59 65 137 143 0 1666 252 1414 1.514 1720 1469 .661 1.437 .598 .523
8 255 266 94 139 161 127 259 259 95 144 165 120 0 0 45 68 16 62 100 84 100 43 288 285 1.268 .789 .727 .669 .735 2.31 32 152 1.07 .73 60 3150 7540 59 65 152 158 0 503 263 240 1.493 490 227 .67 1.376 .578 .461
9 546 235 97 139 449 96 550 232 100 167 453 93 0 0 92 54 29 270 100 0 100 0 545 546 4.677 .214 .205 .185 .213 2.107 52 320 6.177 .22 90 3280 7530 56 65 163 172 0 445 263 182 .405 439 176 2.471 .389 -1.305 -1.364
10 483 333 97 141 386 192 490 338 102 177 393 197 0 0 82 80 32 307 100 5 100 0 578 590 2.01 .497 .501 .461 .486 1.59 52 240 5.139 .3 80 3440 7540 58 66 180 188 0 630 267 363 .941 640 373 1.062 .949 -.087 -.076
11 2348 330 96 150 2252 180 2688 329 98 151 2592 179 0 0 823 86 19 43 100 95 100 82 2432 2771 12.511 .08 .069 .078 .077 1.689 80 333 .076 .83 100 3580 7540 57 67 193 203 0 625 284 341 .151 623 339 6.61 .131 -2.725 -2.936
12 5106 3567 101 154 5005 3413 5337 3609 102 158 5236 3455 0 0 1108 581 20 47 100 100 100 100 8418 8691 1.466 .682 .66 .69 .687 1.147 52 278 .675 .98 90 3720 7540 57 66 207 216 0 6751 291 6460 1.291 6831 6539 .775 1.249 .368 .321
13 1609 1234 120 200 1489 1034 1786 1195 230 632 1666 995 0 0 513 491 191 691 96 86 95 12 2523 2661 1.44 .694 .597 .698 .64 1.604 80 263 .691 .76 100 3870 7530 56 66 222 232 -50 2336 379 1957 1.314 2262 1883 .761 1.13 .394 .177
14 574 1478 117 236 457 1242 584 1523 179 465 467 1287 0 0 225 466 139 505 92 92 76 69 1699 1754 .368 2.718 2.756 2.941 2.85 1.501 120 420 2.729 .9 130 3990 7530 54 67 232 245 -100 2797 447 2351 5.144 2882 2436 .194 5.216 2.363 2.383
15 454 6406 112 221 342 6185 462 6523 127 247 350 6302 0 0 78 1022 85 143 100 100 96 100 6527 6652 .055 18.085 18.006 18.402 17.985 1.253 120 373 18.809 .94 120 4170 7540 56 68 251 263 0 12124 418 11706 34.228 12346 11927 .029 34.078 5.097 5.091
16 4530 9131 123 241 4407 8890 5150 9678 152 363 5027 9437 0 0 1913 3093 96 388 100 100 98 100 13297 14464 .496 2.017 1.877 2.195 2.06 1.344 80 269 1.971 .97 110 4310 7540 56 67 265 276 0 17282 456 16826 3.818 18317 17861 .262 3.553 1.933 1.829
17 3903 15214 122 243 3781 14971 4083 15245 147 342 3961 15002 0 0 2064 8149 96 369 99 99 99 99 18752 18963 .253 3.96 3.787 4.045 4.032 1.186 156 514 3.976 .99 140 4460 7540 55 69 279 293 0 28795 460 28335 7.494 28853 28393 .133 7.168 2.906 2.842
18 137 248 124 241 13 7 114 180 135 286 -10 -61 0 0 69 203 50 177 18 11 8 8 20 -71 1.857 .538 null 2.421 3.238 3.583 80 272 3.796 .9 100 4600 7520 55 65 295 305 -50 469 456 13 1.019 341 -115 .981 null .027 null
19 8922 4977 128 261 8794 4716 9722 5344 148 349 9594 5083 0 0 3516 1987 64 246 100 100 100 100 13510 14677 1.865 .536 .53 .535 .538 1.191 120 341 .539 .99 120 4750 7540 56 68 309 321 0 9420 494 8926 1.015 10114 9620 .985 1.003 .021 .004
20 3997 2433 128 253 3869 2180 4394 2669 141 296 4266 2416 0 0 1241 725 67 153 100 100 100 99 6049 6682 1.775 .563 .566 .566 .565 1.22 120 381 .542 .98 120 4900 7530 55 67 324 336 0 4605 479 4126 1.066 5051 4573 .938 1.072 .093 .1

Total number of rows: 43104

Table truncated, full table size 9579 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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