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Sample GSM84739 Query DataSets for GSM84739
Status Public on Nov 23, 2005
Title FL18 PR 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 (FL18)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL18)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, Follicular Lymphoma
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/25458.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) array@genome.stanford.edu
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
1 384 329 103 74 281 255 393 335 105 81 290 261 0 0 111 105 25 41 97 95 93 95 536 551 1.102 .907 .9 .902 .896 1.783 80 465 .915 .81 110 1830 8400 62 73 33 44 0 339 76 263 .936 345 269 1.069 .928 -.096 -.108
2 300 172 105 73 195 99 265 166 107 77 160 93 0 0 299 51 26 28 98 93 98 80 294 253 1.97 .508 .581 .588 .659 2.319 80 352 .142 .42 100 1980 8400 63 73 49 59 -100 177 75 102 .523 171 96 1.911 .599 -.934 -.739
3 636 455 108 75 528 380 662 446 110 78 554 371 0 0 189 148 26 28 97 100 96 97 908 925 1.389 .72 .67 .706 .667 1.546 80 408 .708 .9 110 2140 8400 62 73 64 75 0 469 77 392 .742 460 382 1.348 .69 -.431 -.535
4 1101 562 109 76 992 486 1181 577 111 80 1072 501 0 0 335 177 41 32 98 100 93 97 1478 1573 2.041 .49 .467 .502 .468 1.635 80 407 .46 .91 100 2300 8390 62 72 81 91 0 579 78 501 .505 595 516 1.98 .482 -.985 -1.053
5 336 200 106 77 230 123 345 201 109 79 239 124 0 0 116 89 27 26 93 85 93 75 353 363 1.87 .535 .519 .451 .458 2.024 80 373 .508 .7 100 2460 8390 62 72 97 107 0 206 79 127 .551 207 128 1.814 .535 -.859 -.903
6 5468 2118 109 79 5359 2039 5847 2254 111 82 5738 2175 0 0 1753 761 29 30 100 98 98 98 7398 7913 2.628 .38 .379 .385 .394 1.806 80 421 .373 .95 110 2610 8380 60 71 111 122 0 2184 81 2102 .392 2324 2242 2.549 .391 -1.35 -1.356
7 332 193 107 82 225 111 353 185 109 84 246 103 0 0 122 71 28 33 88 87 87 72 336 349 2.027 .493 .419 .458 .446 1.977 80 385 .467 .73 100 2770 8390 62 72 128 138 0 199 85 114 .509 191 106 1.966 .432 -.975 -1.212
8 461 219 103 80 358 139 480 212 106 84 377 132 0 0 132 71 24 30 95 93 95 86 497 509 2.576 .388 .35 .339 .374 1.878 80 402 .334 .75 110 2930 8390 61 72 143 154 0 226 82 143 .4 219 136 2.498 .361 -1.321 -1.47
9 180 130 97 76 83 54 183 131 101 81 86 55 0 0 45 47 34 31 86 65 60 45 137 141 1.537 .651 .64 .572 .608 2.72 80 378 .621 .44 100 3080 8390 62 72 159 169 0 134 78 56 .671 135 57 1.491 .659 -.576 -.601
10 105 112 96 79 9 33 91 92 102 94 -5 13 0 0 51 70 42 86 15 9 6 6 42 8 .273 3.667 null 1.301 1.274 2.945 32 185 5.558 .29 70 3230 8420 66 73 175 182 0 115 81 34 3.78 95 13 .265 null 1.918 null
11 278 179 105 80 173 99 284 166 108 89 179 86 0 0 96 67 26 63 90 66 88 32 272 265 1.747 .572 .48 .458 .414 2.178 80 413 .565 .65 100 3390 8380 61 71 190 200 0 185 82 102 .59 171 89 1.695 .495 -.761 -1.014
12 288 131 109 78 179 53 288 133 110 80 179 55 0 0 94 44 25 28 91 68 91 50 232 234 3.377 .296 .307 .244 .294 2.6 80 380 .253 .55 100 3550 8380 61 71 206 216 0 135 80 55 .305 137 57 3.276 .317 -1.712 -1.659
13 276 152 105 75 171 77 299 150 107 78 194 75 0 0 91 54 25 29 88 80 87 63 248 269 2.221 .45 .387 .429 .445 2.776 80 362 .405 .59 100 3710 8380 61 71 222 232 0 157 77 79 .464 155 77 2.154 .399 -1.107 -1.327
14 736 323 107 75 629 248 773 310 111 84 666 235 0 0 263 125 44 43 93 92 91 91 877 901 2.536 .394 .353 .397 .346 2.063 80 351 .355 .82 100 3860 8380 61 71 237 247 0 333 77 256 .406 320 242 2.46 .364 -1.299 -1.459
15 408 227 104 75 304 152 254 152 106 78 150 77 0 0 939 353 40 27 88 82 76 65 456 227 2 .5 .513 .446 .453 2.39 80 429 .339 .84 110 4020 8370 59 70 252 263 -100 234 77 157 .515 157 79 1.94 .529 -.956 -.918
16 442 263 102 75 340 188 459 264 103 80 357 189 0 0 155 80 23 27 93 95 93 92 528 546 1.809 .553 .529 .556 .533 1.691 80 331 .482 .83 100 4170 8380 61 71 268 278 0 271 77 194 .57 272 195 1.754 .546 -.811 -.874
17 238 128 107 79 131 49 236 119 108 83 129 40 0 0 62 47 26 28 96 62 92 35 180 169 2.673 .374 .31 .313 .315 2.71 80 352 .334 .46 100 4310 8380 61 71 282 292 0 132 81 51 .386 123 41 2.593 .32 -1.375 -1.645
18 376 121 107 79 269 42 383 111 109 82 276 32 0 0 100 47 24 26 97 52 96 36 311 308 6.405 .156 .116 .144 .171 2.525 80 370 .137 .42 100 4470 8380 61 71 298 308 0 125 81 43 .161 114 33 6.213 .12 -2.635 -3.065
19 409 309 110 78 299 231 428 301 108 80 318 223 0 0 121 108 24 26 96 100 92 97 530 541 1.294 .773 .701 .77 .738 1.837 80 404 .721 .82 110 4620 8380 60 71 312 323 0 319 80 238 .796 310 230 1.256 .723 -.328 -.468
20 339 131 106 76 233 55 355 129 107 79 249 53 0 0 97 45 25 26 93 75 93 50 288 302 4.236 .236 .213 .223 .25 2.2 80 470 .204 .53 110 4780 8370 59 70 328 339 0 135 78 57 .243 133 55 4.109 .219 -2.039 -2.188

Total number of rows: 37632

Table truncated, full table size 8035 Kbytes.




Supplementary data files not provided
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