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Sample GSM475055 Query DataSets for GSM475055
Status Public on Apr 12, 2010
Title LLAT 1A
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 1A
Organism Homo sapiens
Characteristics individual: patient1
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/2003-04/40060.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
1 412 446 107 132 305 314 400 450 118 147 293 318 0 0 65 103 73 114 100 90 100 84 619 611 .971 1.03 1.085 .983 1.02 1.513 32 210 1.307 .88 70 2060 8640 64 71 58 65 0 706 209 497 1.63 712 503 .614 1.718 .705 .781
2 4455 431 108 129 4347 302 4594 441 122 146 4486 312 0 0 1432 138 74 105 100 92 100 73 4649 4798 14.394 .069 .07 .066 .068 1.611 52 284 .067 .8 80 2210 8640 64 72 73 81 0 682 204 478 .11 698 494 9.093 .11 -3.185 -3.183
3 705 576 99 122 606 454 709 564 101 127 610 442 0 0 137 141 20 42 100 100 100 100 1060 1052 1.335 .749 .725 .727 .727 1.373 32 206 .764 .92 70 2360 8640 64 71 88 95 0 912 193 719 1.186 893 700 .843 1.147 .246 .198
4 980 358 98 118 882 240 1009 360 100 127 911 242 0 0 254 127 19 44 100 93 100 84 1122 1153 3.675 .272 .266 .225 .279 1.99 32 208 .274 .84 70 2500 8630 63 70 102 109 0 567 187 380 .431 570 383 2.321 .421 -1.215 -1.25
5 3210 1267 102 122 3108 1145 3322 1422 103 126 3220 1300 0 0 1511 563 19 41 100 98 100 96 4253 4520 2.714 .368 .404 .36 .358 1.618 52 265 .36 .97 80 2640 8640 64 72 116 124 0 2006 193 1813 .583 2251 2058 1.715 .639 -.778 -.646
6 356 392 103 119 253 273 357 382 103 126 254 263 0 0 70 90 19 43 100 100 100 100 526 517 .927 1.079 1.035 1.068 1.011 1.483 32 171 1.16 .82 60 2790 8640 65 71 132 138 0 621 188 432 1.708 605 416 .585 1.639 .772 .713
7 1515 1246 103 131 1412 1115 1592 1315 104 134 1489 1184 0 0 361 353 21 46 100 100 100 100 2527 2673 1.266 .79 .795 .77 .789 1.428 32 164 .799 .95 60 2940 8640 65 71 147 153 0 1972 207 1765 1.25 2082 1874 .8 1.259 .322 .332
8 605 535 101 127 504 408 606 538 101 132 505 411 0 0 125 118 17 46 100 100 100 100 912 916 1.235 .81 .814 .805 .784 1.394 32 200 .807 .89 70 3080 8640 64 71 160 167 0 847 201 646 1.282 852 651 .78 1.288 .358 .366
9 923 554 102 122 821 432 919 553 106 128 817 431 0 0 119 130 36 43 100 100 100 100 1253 1248 1.9 .526 .528 .504 .528 1.398 52 317 .538 .92 90 3220 8630 62 71 173 182 0 877 193 684 .833 875 682 1.201 .835 -.264 -.26
10 949 601 102 124 847 477 890 574 108 137 788 450 0 0 196 134 63 82 100 100 100 100 1324 1238 1.776 .563 .571 .553 .545 1.284 52 301 .543 .9 90 3370 8630 62 71 188 197 0 951 196 755 .892 909 712 1.122 .904 -.166 -.146
11 3788 630 104 127 3684 503 3989 644 155 141 3885 517 0 0 659 161 330 93 100 98 100 96 4187 4402 7.324 .137 .133 .13 .134 1.295 52 305 .137 .52 90 3510 8620 61 70 202 211 0 997 201 796 .216 1019 818 4.627 .211 -2.21 -2.247
12 4561 5560 105 124 4456 5436 4867 6069 122 131 4762 5945 0 0 1540 1981 112 51 100 100 100 100 9892 10707 .82 1.22 1.248 1.192 1.246 1.386 80 326 1.239 .97 100 3670 8630 62 72 218 228 0 8802 196 8605 1.931 9607 9411 .518 1.976 .949 .983
13 1948 3042 108 128 1840 2914 1968 3161 114 134 1860 3033 0 0 335 673 32 46 100 100 100 100 4754 4893 .631 1.584 1.631 1.552 1.614 1.286 80 271 1.629 .97 100 3810 8630 62 72 232 242 0 4816 203 4613 2.507 5004 4801 .399 2.581 1.326 1.368
14 609 695 109 150 500 545 579 671 110 172 470 521 0 0 183 189 23 109 100 100 100 96 1045 991 .917 1.09 1.109 1.092 1.098 1.412 80 339 1.166 .89 110 3950 8630 61 72 245 256 0 1100 237 863 1.726 1062 825 .58 1.755 .787 .811
15 540 16630 112 167 428 16463 558 16613 114 185 446 16446 0 0 137 4641 25 98 100 100 97 100 16891 16892 .026 38.465 36.874 38.714 37.595 1.224 120 469 39.126 .96 130 4100 8640 61 74 259 272 0 26326 264 26062 60.891 26299 26035 .016 58.374 5.928 5.867
16 5069 6494 116 165 4953 6329 5736 6947 117 172 5620 6782 0 0 1984 2137 28 50 100 100 100 100 11282 12402 .783 1.278 1.207 1.368 1.287 1.419 80 240 1.24 .97 100 4250 8640 63 73 276 286 0 10280 261 10019 2.023 10997 10736 .494 1.91 1.016 .934
17 7448 8448 112 167 7336 8281 8022 8572 114 172 7910 8405 0 0 3029 3964 24 48 100 100 100 100 15617 16315 .886 1.129 1.063 1.068 1.137 1.334 120 396 1.171 .98 130 4390 8630 60 73 288 301 0 13373 264 13109 1.787 13570 13305 .56 1.682 .838 .75
18 127 160 106 157 21 3 113 150 109 163 7 -7 0 0 44 65 20 45 31 18 21 6 24 0 7 .143 null 2.133 2.304 2.87 80 264 4.907 .24 100 4530 8620 61 71 304 314 -50 253 249 5 .226 237 -11 4.422 null -2.145 null
19 12114 7780 107 156 12007 7624 12852 7589 140 166 12745 7433 0 0 4577 3606 170 76 100 100 100 100 19631 20178 1.575 .635 .583 .607 .637 1.293 120 362 .662 .98 120 4690 8630 61 73 319 331 0 12316 247 12069 1.005 12014 11767 .995 .923 .007 -.115
20 5097 3733 114 156 4983 3577 5822 4279 159 168 5708 4123 0 0 1913 1480 180 80 100 100 100 100 8560 9831 1.393 .718 .722 .709 .729 1.261 120 357 .731 .99 120 4830 8630 61 73 333 345 0 5909 247 5663 1.136 6774 6527 .88 1.143 .184 .193

Total number of rows: 43104

Table truncated, full table size 9925 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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