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Sample GSM475048 Query DataSets for GSM475048
Status Public on Apr 12, 2010
Title LLAT 6A
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 6A
Organism Homo sapiens
Characteristics individual: patient6
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/2003-05/40696.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
1 146 168 77 83 69 85 147 167 78 86 70 84 0 0 24 45 18 31 96 90 93 71 154 154 .812 1.232 1.2 1.133 1.229 1.862 32 164 1.428 .67 60 1470 7200 49 55 48 54 0 179 88 90 1.311 178 89 .763 1.277 .391 .353
2 1391 149 76 80 1315 69 1342 154 77 84 1266 74 0 0 613 55 17 34 100 65 100 51 1384 1340 19.058 .052 .058 .055 .06 1.911 52 277 .051 .62 80 1620 7200 48 56 62 70 0 159 85 73 .056 164 79 17.904 .062 -4.162 -4.006
3 211 205 72 83 139 122 205 209 74 86 133 126 0 0 88 77 15 32 96 87 90 78 261 259 1.139 .878 .947 .901 .985 1.963 32 159 .932 .75 60 1760 7210 50 56 77 83 0 218 88 130 .934 222 134 1.07 1.008 -.098 .012
4 336 120 74 82 262 38 332 119 74 88 258 37 0 0 89 43 16 33 100 50 100 25 300 295 6.895 .145 .143 .14 .191 2.355 32 164 .142 .41 60 1910 7200 49 55 92 98 0 128 87 40 .154 127 39 6.477 .153 -2.695 -2.712
5 1299 507 76 82 1223 425 1524 553 77 85 1448 471 0 0 712 231 19 28 100 98 100 94 1648 1919 2.878 .348 .325 .351 .328 1.742 52 296 .333 .97 80 2060 7200 48 56 106 114 0 540 87 452 .37 589 501 2.703 .346 -1.435 -1.53
6 144 139 79 87 65 52 152 141 79 88 73 54 0 0 34 26 19 26 91 75 83 50 117 127 1.25 .8 .74 .665 .674 2.25 12 104 1.588 .46 50 2200 7200 49 54 121 126 0 148 93 55 .852 150 57 1.174 .787 -.232 -.345
7 662 432 73 79 589 353 689 460 75 83 616 381 0 0 222 130 17 28 100 100 100 100 942 997 1.669 .599 .619 .596 .556 1.38 32 156 .587 .93 60 2350 7210 50 56 136 142 0 460 84 376 .638 490 406 1.568 .658 -.648 -.603
8 231 211 74 84 157 127 231 219 76 87 157 135 0 0 51 64 17 28 96 90 96 84 284 292 1.236 .809 .86 .755 .869 1.998 32 164 .974 .85 60 2490 7200 49 55 150 156 0 225 89 135 .861 233 144 1.161 .915 -.216 -.128
9 393 235 75 85 318 150 393 229 78 89 318 144 0 0 70 53 23 31 100 98 100 98 468 462 2.12 .472 .453 .45 .467 1.395 52 314 .493 .86 90 2640 7190 46 55 163 172 0 250 90 160 .502 244 153 1.992 .482 -.994 -1.053
10 560 361 75 82 485 279 506 330 84 90 431 248 0 0 186 109 62 46 100 100 100 100 764 679 1.738 .575 .575 .574 .573 1.355 52 293 .565 .91 90 2780 7180 45 54 177 186 0 384 87 297 .612 351 264 1.633 .613 -.708 -.707
11 1800 261 72 83 1728 178 1811 257 85 88 1739 174 0 0 216 64 91 35 100 100 100 96 1906 1913 9.708 .103 .1 .096 .1 1.454 52 313 .101 .86 90 2930 7190 46 55 192 201 0 278 88 189 .11 274 185 9.12 .107 -3.189 -3.231
12 1660 1882 73 82 1587 1800 1838 1978 76 86 1765 1896 0 0 807 797 17 30 100 100 98 100 3387 3661 .882 1.134 1.074 1.247 1.149 1.499 80 341 1.103 .98 100 3080 7200 47 57 207 217 0 2003 87 1916 1.207 2106 2018 .828 1.143 .272 .193
13 1192 1514 75 86 1117 1428 1218 1536 77 92 1143 1450 0 0 327 464 17 35 100 100 100 100 2545 2593 .782 1.278 1.269 1.268 1.271 1.208 80 310 1.304 .97 100 3220 7190 46 56 221 231 0 1612 92 1520 1.361 1635 1543 .735 1.35 .444 .433
14 409 450 78 96 331 354 434 462 84 106 356 366 0 0 117 126 38 64 100 100 100 96 685 722 .935 1.069 1.028 1.072 1.095 1.383 80 281 1.084 .91 100 3370 7190 46 56 236 246 0 479 102 377 1.138 492 390 .878 1.094 .187 .13
15 253 18806 82 111 171 18695 263 20095 88 134 181 19984 0 0 79 8403 36 116 92 100 85 100 18866 20165 .009 109.327 110.409 81.411 84.863 1.173 120 365 117.944 .92 120 3510 7200 46 58 249 261 0 20018 118 19900 116.376 21390 21272 .009 117.527 6.863 6.877
16 2097 5040 88 133 2009 4907 2001 4842 91 156 1913 4709 0 0 800 1831 24 121 100 100 100 100 6916 6622 .409 2.443 2.462 2.468 2.413 1.197 80 247 2.443 .98 100 3660 7200 47 57 265 275 0 5365 142 5223 2.6 5154 5013 .385 2.62 1.378 1.39
17 3903 7894 87 128 3816 7766 4037 8053 91 144 3950 7925 0 0 1927 3855 33 98 100 100 100 100 11582 11875 .491 2.035 2.006 2.061 2.012 1.223 120 445 2.03 .99 130 3800 7190 44 57 277 290 0 8403 136 8267 2.166 8572 8436 .462 2.136 1.115 1.095
18 122 134 82 111 40 23 93 128 89 126 11 17 0 0 111 52 37 65 27 23 16 3 63 28 1.739 .575 1.545 1.502 1.541 4.308 80 307 .406 .16 100 3950 7180 45 55 294 304 -50 143 118 24 .612 136 18 1.634 1.645 -.708 .718
19 5887 4966 80 102 5807 4864 5581 4437 83 109 5501 4335 0 0 1632 1626 23 41 100 100 100 100 10671 9836 1.194 .838 .788 .826 .817 1.159 80 288 .851 .98 100 4100 7190 46 56 309 319 0 5286 109 5178 .892 4723 4614 1.122 .839 -.166 -.254
20 2916 2533 78 116 2838 2417 3335 2887 84 122 3257 2771 0 0 1320 1024 31 47 100 100 100 100 5255 6028 1.174 .852 .851 .878 .854 1.226 120 458 .825 .99 120 4240 7190 45 57 322 334 0 2696 123 2573 .907 3073 2950 1.103 .906 -.142 -.143

Total number of rows: 43104

Table truncated, full table size 9562 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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