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Sample GSM84721 Query DataSets for GSM84721
Status Public on Nov 23, 2005
Title FL3 NR LC
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Follicular lymphoma (FL3)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18862.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 22, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3113
Series (2)
GSE3647 Follicular lymphoma lymph node
GSE4351 Variation in gene expression patterns in follicular lymphoma and the response to rituximab

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 61 50 61 51 0 -1 59 41 64 53 -2 -10 0 0 16 20 16 21 13 15 3 3 -1 -12 null null null 1.225 1.3 3.16 80 409 23.65 .03 100 1530 9450 72 82 48 58 -50 71 73 -1 null 59 null null null null null
2 60 48 62 49 -2 -1 59 47 64 52 -3 -2 0 0 15 20 17 21 13 10 2 3 -3 -5 null null null .995 1 3.834 80 304 3.579 .06 100 1690 9450 72 82 64 74 -50 69 70 -1 null 67 null null null null null
3 630 587 63 49 567 538 534 454 67 52 471 405 0 0 353 412 24 21 98 98 98 98 1105 876 1.054 .949 .86 .832 .916 1.925 156 662 1.007 .92 150 1820 9460 70 85 74 89 0 839 70 769 1.356 649 579 .738 1.228 .439 .297
4 1904 565 64 47 1840 518 2023 516 67 49 1959 469 0 0 510 200 21 20 100 100 100 100 2358 2428 3.552 .282 .239 .279 .266 1.527 80 396 .269 .9 110 2000 9450 71 82 94 105 0 807 67 740 .402 737 670 2.486 .342 -1.314 -1.548
5 445 263 64 56 381 207 421 232 66 58 357 176 0 0 150 114 18 21 97 100 97 98 588 533 1.841 .543 .493 .52 .477 1.732 80 372 .523 .85 100 2160 9450 72 82 111 121 0 376 80 296 .776 331 251 1.288 .704 -.366 -.506
6 10176 2265 62 53 10114 2212 11092 2323 64 55 11030 2270 0 0 3030 887 17 22 100 100 100 100 12326 13300 4.572 .219 .206 .221 .215 1.88 80 410 .212 .9 110 2320 9450 71 82 126 137 0 3236 76 3160 .312 3319 3243 3.201 .294 -1.678 -1.766
7 384 140 62 49 322 91 379 133 63 52 317 84 0 0 148 71 17 21 96 83 96 73 413 401 3.538 .283 .265 .237 .272 2.491 80 359 .282 .77 100 2480 9450 72 82 143 153 0 200 70 130 .404 190 120 2.477 .379 -1.309 -1.401
8 68 62 63 49 5 13 69 56 64 52 6 7 0 0 17 23 17 20 21 32 3 15 18 13 .385 2.6 1.167 1.05 .818 2.902 80 388 18.356 .03 100 2630 9450 72 82 158 168 -50 89 70 19 3.714 80 10 .269 1.667 1.893 .737
9 186 262 63 46 123 216 185 252 65 50 122 206 0 0 49 109 16 20 97 98 93 97 339 328 .569 1.756 1.689 1.672 1.637 1.763 80 416 2.123 .79 110 2800 9450 71 82 174 185 0 374 66 309 2.509 360 294 .399 2.412 1.327 1.27
10 76 60 63 53 13 7 63 51 65 56 0 -2 0 0 94 46 17 21 21 20 3 6 20 -2 1.857 .538 null 1.139 1 3.099 80 359 .285 .52 100 2940 9450 72 82 189 199 -50 86 76 10 .769 73 null 1.3 null -.379 null
11 231 166 63 50 168 116 228 162 67 53 165 112 0 0 69 68 18 22 96 97 96 87 284 277 1.448 .69 .679 .663 .646 1.965 80 350 .694 .75 100 3110 9450 72 82 206 216 0 237 71 166 .986 231 160 1.014 .97 -.02 -.044
12 71 60 64 49 7 11 68 53 67 51 4 4 0 0 23 31 18 19 22 28 8 15 18 8 .636 1.571 1 1.197 1.442 3.929 80 350 9.229 .05 100 3250 9450 72 82 220 230 -50 86 70 16 2.245 76 6 .445 1.429 1.167 .515
13 323 296 66 54 257 242 324 280 68 56 258 226 0 0 106 126 17 22 96 98 96 97 499 484 1.062 .942 .876 .888 .912 1.937 80 430 .988 .79 100 3420 9450 72 82 237 247 0 423 77 346 1.345 400 323 .743 1.251 .428 .324
14 439 500 65 49 374 451 157 229 69 53 92 180 0 0 616 572 21 22 68 84 59 78 825 272 .829 1.206 1.957 1.707 1.389 3.746 32 213 1.028 .78 70 3580 9440 72 79 254 261 -100 714 70 644 1.723 327 257 .58 2.795 .785 1.483
15 309 241 64 54 245 187 324 234 67 56 260 180 0 0 100 88 19 21 96 97 95 95 432 440 1.31 .763 .692 .764 .748 2.151 80 451 .739 .76 110 3730 9450 71 82 267 278 0 344 77 267 1.09 334 257 .917 .989 .125 -.016
16 1109 1489 63 55 1046 1434 1154 1559 66 57 1091 1504 0 0 245 482 18 21 100 100 100 100 2480 2595 .729 1.371 1.379 1.293 1.371 1.605 80 416 1.475 .92 110 3890 9440 70 81 283 294 0 2127 79 2049 1.958 2227 2149 .511 1.969 .97 .978
17 64 44 65 51 -1 -7 63 42 67 53 -2 -9 0 0 19 16 19 19 20 10 1 1 -8 -11 null null null 1.112 1 3.25 80 365 3.235 .04 100 4030 9440 71 81 298 308 -50 63 73 -10 null 60 null null null null null
18 306 213 65 54 241 159 300 199 66 57 235 145 0 0 90 76 16 20 98 100 98 96 400 380 1.516 .66 .617 .642 .654 1.836 80 378 .627 .8 100 4200 9440 71 81 315 325 0 304 77 227 .943 284 207 1.061 .881 -.085 -.182
19 60 57 64 53 -4 4 62 54 70 55 -2 1 0 0 14 24 26 22 1 22 0 10 0 -1 null null null 1.474 1.278 4.621 80 378 .818 .15 100 4350 9440 71 81 330 340 -50 81 76 6 null 77 1 null null null null
20 532 378 64 55 468 323 510 363 71 57 446 308 0 0 172 162 29 22 100 100 100 100 791 754 1.449 .69 .691 .644 .672 1.502 80 434 .722 .9 110 4520 9440 70 81 346 357 0 540 79 461 .986 519 440 1.014 .987 -.02 -.02

Total number of rows: 37632

Table truncated, full table size 7953 Kbytes.




Supplementary data files not provided
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