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Sample GSM475053 Query DataSets for GSM475053
Status Public on Apr 12, 2010
Title LLAT 4A
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 4A
Organism Homo sapiens
Characteristics individual: patient4
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/2003-04/40073.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
1 231 290 79 98 152 192 229 279 80 99 150 181 0 0 63 77 13 26 96 100 96 94 344 331 .792 1.263 1.207 1.377 1.199 2.287 52 254 1.342 .88 80 2060 8180 78 86 50 58 0 598 202 396 2.603 575 373 .384 2.487 1.38 1.314
2 3596 280 81 98 3515 182 3624 295 82 101 3543 197 0 0 1299 100 16 28 100 88 100 88 3697 3740 19.313 .052 .056 .054 .057 1.366 52 274 .051 .89 80 2210 8170 77 85 65 73 0 577 202 375 .107 608 406 9.371 .115 -3.228 -3.125
3 529 409 80 97 449 312 581 434 80 99 501 337 0 0 150 136 14 27 100 100 100 96 761 838 1.439 .695 .673 .643 .673 1.649 32 198 .717 .93 70 2360 8170 77 84 80 87 0 843 200 643 1.432 894 695 .698 1.386 .518 .471
4 659 217 80 99 579 118 694 225 80 107 614 126 0 0 240 75 16 45 100 80 100 61 697 740 4.907 .204 .205 .195 .222 1.912 52 249 .205 .8 80 2500 8170 77 85 94 102 0 447 204 243 .42 464 260 2.381 .423 -1.251 -1.241
5 3442 825 81 103 3361 722 3610 890 86 105 3529 787 0 0 842 236 29 29 100 100 100 100 4083 4316 4.655 .215 .223 .201 .221 1.455 32 196 .223 .96 70 2630 8170 77 84 107 114 0 1700 212 1488 .443 1834 1622 2.259 .46 -1.175 -1.122
6 279 299 76 102 203 197 290 295 78 103 214 193 0 0 74 76 14 28 100 100 96 100 400 407 1.03 .97 .902 1.003 .976 1.846 32 221 1.001 .87 70 2800 8170 77 84 124 131 0 616 210 406 2 608 398 .5 1.859 1 .894
7 1344 756 78 100 1266 656 1363 819 80 103 1285 719 0 0 313 222 14 25 100 100 100 100 1922 2004 1.93 .518 .56 .494 .51 1.406 32 208 .521 .95 70 2940 8170 77 84 138 145 0 1558 206 1352 1.068 1688 1482 .936 1.153 .095 .206
8 423 349 77 97 346 252 416 357 77 98 339 260 0 0 57 60 14 26 100 100 100 100 598 599 1.373 .728 .767 .718 .738 1.282 32 188 .739 .92 70 3080 8170 77 84 152 159 0 719 200 519 1.501 736 536 .666 1.581 .586 .661
9 727 320 77 101 650 219 724 314 83 103 647 213 0 0 85 63 34 31 100 100 100 100 869 860 2.968 .337 .329 .326 .322 1.344 52 305 .334 .91 90 3220 8160 75 84 165 174 0 660 208 451 .694 647 439 1.44 .678 -.526 -.56
10 752 472 77 104 675 368 737 466 79 105 660 362 0 0 137 87 18 27 100 100 100 100 1043 1022 1.834 .545 .548 .54 .532 1.268 52 222 .556 .94 80 3370 8160 76 84 181 189 0 973 214 758 1.124 960 746 .89 1.13 .168 .177
11 2842 370 79 106 2763 264 3087 399 80 107 3008 293 0 0 756 114 15 27 100 97 100 92 3027 3301 10.466 .096 .097 .086 .098 1.507 80 331 .098 .95 100 3510 8160 75 85 194 204 0 763 218 544 .197 822 604 5.078 .201 -2.344 -2.317
12 3968 4526 80 114 3888 4412 4397 5003 84 116 4317 4889 0 0 1325 1436 18 32 100 100 100 100 8300 9206 .881 1.135 1.132 1.153 1.126 1.282 80 301 1.127 .99 100 3660 8170 76 86 209 219 0 9328 235 9093 2.339 10311 10076 .428 2.334 1.226 1.223
13 1690 1923 82 120 1608 1803 1757 2026 85 125 1675 1906 0 0 509 552 20 39 100 100 100 100 3411 3581 .892 1.121 1.138 1.134 1.129 1.266 80 307 1.125 .98 110 3800 8170 75 86 222 233 0 3963 247 3716 2.311 4176 3928 .433 2.345 1.208 1.23
14 347 469 84 118 263 351 337 451 86 125 253 333 0 0 134 132 18 37 100 100 99 100 614 586 .749 1.335 1.316 1.446 1.355 1.517 120 342 1.252 .89 120 3950 8170 75 87 237 249 0 967 243 723 2.751 929 686 .364 2.713 1.46 1.44
15 373 11107 86 126 287 10981 414 12636 91 131 328 12510 0 0 149 5677 38 40 91 100 85 100 11268 12838 .026 38.261 38.14 36.494 37.718 1.339 156 505 38.94 .98 140 4090 8170 74 88 250 264 0 22891 260 22631 78.855 26042 25783 .013 78.606 6.301 6.297
16 4297 6882 90 135 4207 6747 4517 7191 95 140 4427 7056 0 0 1461 2117 31 41 100 100 100 100 10954 11483 .624 1.604 1.594 1.64 1.655 1.208 80 225 1.589 .98 100 4240 8170 76 86 267 277 0 14184 278 13905 3.305 14820 14542 .303 3.285 1.725 1.716
17 5950 7378 90 143 5860 7235 6424 8275 96 147 6334 8132 0 0 2430 3093 46 61 100 100 100 100 13095 14466 .81 1.235 1.284 1.213 1.223 1.153 120 408 1.244 .99 130 4380 8160 73 86 279 292 0 15206 295 14911 2.545 17055 16760 .393 2.646 1.347 1.404
18 106 150 91 143 15 7 94 139 97 150 3 -4 0 0 42 51 49 70 15 11 7 3 22 -1 2.143 .467 null 1.195 1.315 4.184 80 276 2.388 .4 100 4530 8150 74 84 296 306 -50 309 295 14 .962 286 -8 1.04 null -.056 null
19 8878 4784 90 143 8788 4641 9204 4919 114 161 9114 4776 0 0 3213 2060 158 99 100 100 100 100 13429 13890 1.894 .528 .524 .507 .515 1.165 120 423 .545 .99 130 4680 8160 73 86 309 322 0 9860 295 9565 1.088 10138 9843 .919 1.08 .122 .111
20 4744 3067 95 156 4649 2911 4904 3269 145 186 4809 3113 0 0 945 743 210 128 100 100 100 100 7560 7922 1.597 .626 .647 .614 .624 1.175 80 317 .632 .98 110 4820 8150 73 84 324 335 0 6321 322 5999 1.29 6737 6416 .775 1.334 .368 .416

Total number of rows: 43104

Table truncated, full table size 9587 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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