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Sample GSM475051 Query DataSets for GSM475051
Status Public on Apr 12, 2010
Title LLAT 9
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 9
Organism Homo sapiens
Characteristics individual: patient7
treatment: no treatment
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/2003-05/40723.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
1 324 337 123 99 201 238 322 332 144 122 199 233 0 0 66 76 164 114 71 100 3 53 439 432 .845 1.184 1.171 1.189 1.16 1.503 32 148 1.113 .72 60 1470 8630 60 66 44 50 0 496 146 351 1.744 489 343 .573 1.725 .803 .787
2 1919 254 125 111 1794 143 1962 269 136 114 1837 158 0 0 949 88 111 40 100 88 100 73 1937 1995 12.545 .08 .086 .08 .08 1.864 52 276 .07 .79 80 1620 8620 58 66 58 66 0 374 164 211 .117 396 233 8.516 .127 -3.09 -2.98
3 575 399 119 111 456 288 558 391 123 119 439 280 0 0 78 99 31 41 100 100 100 100 744 719 1.583 .632 .638 .604 .66 1.455 12 104 .682 .89 50 1760 8620 59 64 73 78 0 588 164 424 .93 576 412 1.075 .94 -.104 -.09
4 509 280 122 114 387 166 483 273 123 118 361 159 0 0 121 95 25 39 100 93 100 84 553 520 2.331 .429 .44 .391 .407 1.749 32 164 .403 .73 60 1910 8620 59 65 88 94 0 412 168 245 .632 402 234 1.582 .649 -.662 -.624
5 2459 858 124 116 2335 742 2774 868 127 121 2650 752 0 0 891 307 28 45 100 96 100 96 3077 3402 3.147 .318 .284 .322 .305 1.667 32 220 .309 .95 70 2050 8620 58 65 101 108 0 1264 171 1093 .468 1279 1108 2.136 .418 -1.095 -1.258
6 231 302 127 125 104 177 240 293 128 132 113 168 0 0 42 107 24 46 96 87 90 84 281 281 .588 1.702 1.487 1.455 1.789 2.257 32 176 2.225 .72 60 2210 8620 59 65 118 124 0 445 184 261 2.507 432 247 .399 2.19 1.326 1.131
7 1110 747 127 133 983 614 1108 747 128 137 981 614 0 0 120 131 23 48 100 100 100 100 1597 1595 1.601 .625 .626 .616 .602 1.286 12 104 .53 .9 50 2340 8620 59 64 131 136 0 1100 196 905 .92 1100 905 1.087 .922 -.12 -.117
8 476 439 120 128 356 311 477 410 124 131 357 282 0 0 98 127 25 40 100 96 100 96 667 639 1.145 .874 .79 .807 .784 1.63 32 164 .943 .86 60 2490 8620 59 65 146 152 0 647 189 458 1.287 604 415 .777 1.164 .364 .219
9 769 532 125 122 644 410 768 533 127 130 643 411 0 0 137 118 29 49 100 100 100 100 1054 1054 1.571 .637 .639 .624 .61 1.349 52 257 .629 .92 80 2640 8610 57 65 160 168 0 784 180 604 .938 785 605 1.066 .942 -.092 -.087
10 1097 786 125 130 972 656 963 714 126 135 838 584 0 0 534 279 29 44 100 100 100 100 1628 1422 1.482 .675 .697 .697 .698 1.326 52 282 .675 .89 90 2780 8610 56 65 173 182 0 1158 192 966 .994 1052 860 1.006 1.027 -.008 .038
11 2869 548 122 134 2747 414 2824 539 135 140 2702 405 0 0 351 98 87 49 100 100 100 100 3161 3107 6.635 .151 .15 .147 .146 1.259 52 305 .147 .93 90 2930 8600 55 64 188 197 0 807 197 610 .222 794 597 4.504 .221 -2.171 -2.179
12 3655 3234 132 144 3523 3090 3623 3352 137 150 3491 3208 0 0 897 869 36 54 100 100 100 100 6613 6699 1.14 .877 .919 .865 .884 1.158 52 302 .883 .97 90 3080 8600 55 64 203 212 0 4764 212 4552 1.292 4938 4726 .774 1.354 .37 .437
13 1762 1536 132 135 1630 1401 1771 1532 132 142 1639 1397 0 0 551 425 30 56 100 100 100 100 3031 3036 1.163 .86 .852 .873 .85 1.335 80 336 .854 .94 100 3220 8610 56 66 217 227 0 2263 199 2064 1.266 2257 2058 .79 1.256 .341 .328
14 1104 1089 130 134 974 955 1127 1109 130 147 997 975 0 0 235 209 27 72 100 100 100 100 1929 1972 1.02 .98 .978 .989 1.014 1.202 52 294 1.016 .94 90 3360 8600 55 64 231 240 0 1604 197 1407 1.444 1634 1436 .692 1.441 .531 .527
15 1056 3086 130 140 926 2946 1035 3101 134 150 905 2961 0 0 161 421 33 66 100 100 100 100 3872 3866 .314 3.181 3.272 3.198 3.159 1.172 80 381 3.261 .96 110 3510 8610 55 66 245 256 0 4546 206 4340 4.687 4568 4362 .213 4.82 2.229 2.269
16 5887 4977 134 159 5753 4818 5386 4737 139 166 5252 4578 0 0 2113 1593 34 65 100 100 100 100 10571 9830 1.194 .837 .872 .845 .844 1.201 80 278 .82 .97 100 3660 8610 56 66 261 271 0 7332 234 7098 1.234 6979 6744 .811 1.284 .303 .361
17 4724 8605 138 164 4586 8441 5508 9538 141 175 5370 9374 0 0 2503 4437 34 71 100 100 100 100 13027 14744 .543 1.841 1.746 1.874 1.831 1.268 120 408 1.836 .98 130 3800 8620 55 68 273 286 0 12677 242 12435 2.712 14051 13810 .369 2.572 1.439 1.363
18 151 188 135 156 16 32 145 183 145 165 10 27 0 0 42 65 55 70 13 27 3 6 48 37 .5 2 2.7 1.838 1.536 3.693 80 284 5.397 .28 100 3940 8600 55 65 289 299 -50 277 230 47 2.946 270 40 .339 3.978 1.559 1.992
19 6038 3352 132 151 5906 3201 6941 3567 144 158 6809 3416 0 0 3638 1791 59 58 99 99 97 98 9107 10225 1.845 .542 .502 .619 .519 1.625 120 375 .515 .97 120 4100 8610 55 67 304 316 0 4938 222 4716 .798 5255 5032 1.252 .739 -.325 -.436
20 6022 2871 139 164 5883 2707 6327 2963 153 175 6188 2799 0 0 1401 697 62 76 100 100 100 100 8590 8987 2.173 .46 .452 .456 .457 1.207 80 319 .454 .97 110 4240 8610 55 66 318 329 0 4230 242 3988 .678 4365 4123 1.475 .666 -.561 -.586

Total number of rows: 43104

Table truncated, full table size 9841 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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