NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84711 Query DataSets for GSM84711
Status Public on Nov 23, 2005
Title FL8 PR
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 (FL8)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL8)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14559.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 GPL3042
Series (2)
GSE3646 Follicular lymphoma and normal lymphoid tissue comparisons
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
1 915 1212 111 109 804 1103 850 1165 113 113 739 1056 0 0 449 484 25 35 100 100 100 100 1907 1795 .729 1.372 1.429 1.485 1.471 1.516 52 275 1.314 .91 80 1980 7940 110 118 138 146 -100 1757 158 1599 1.988 1688 1530 .503 2.071 .991 1.05
2 582 491 108 108 474 383 251 261 111 109 143 153 0 0 679 502 23 31 93 84 68 71 857 296 1.238 .808 1.07 .976 .888 2.16 32 161 .833 .9 60 2120 7930 110 116 153 159 -100 712 157 555 1.171 378 222 .854 1.551 .228 .633
3 4519 1647 107 108 4412 1539 4268 1577 109 110 4161 1469 0 0 2674 906 20 27 100 100 100 100 5951 5630 2.867 .349 .353 .364 .339 1.707 52 219 .334 .96 80 2260 7930 109 117 166 174 0 2387 157 2230 .506 2286 2129 1.978 .512 -.984 -.967
4 297 202 107 113 190 89 119 119 112 120 12 6 0 0 487 227 66 67 21 20 18 17 279 18 2.135 .468 .5 .955 .946 3.607 80 371 .448 .91 100 2380 7910 106 116 177 187 -50 293 164 129 .679 172 9 1.473 .725 -.559 -.465
5 2205 846 109 108 2096 738 2111 887 118 112 2002 779 0 0 1091 407 67 32 100 100 100 100 2834 2781 2.84 .352 .389 .34 .354 1.335 32 171 .35 .95 70 2540 7920 108 115 194 201 0 1226 157 1070 .51 1286 1129 1.96 .564 -.971 -.826
6 284 213 109 117 175 96 115 121 115 120 6 4 0 0 479 275 48 33 20 26 17 20 271 10 1.823 .549 .667 1.269 .909 3.319 80 375 .575 .91 100 2650 7910 106 116 204 214 -50 309 170 139 .795 175 6 1.258 .966 -.331 -.05
7 1844 875 111 115 1733 760 1113 474 114 119 1002 359 0 0 1506 773 30 35 100 100 100 100 2493 1361 2.28 .439 .358 .365 .341 1.624 52 258 .435 .9 80 2810 7930 109 117 221 229 0 1268 167 1101 .636 687 520 1.573 .519 -.654 -.945
8 649 322 114 121 535 201 556 277 131 191 442 156 0 0 393 201 102 438 88 11 78 0 736 598 2.662 .376 .353 .299 .328 2.362 52 225 2.424 .38 80 2940 7920 108 116 234 242 -100 467 175 291 .544 401 226 1.837 .512 -.877 -.967
9 587 337 112 125 475 212 239 202 149 167 127 77 0 0 767 322 257 252 36 21 25 15 687 204 2.241 .446 .606 .645 .564 4.056 52 207 .786 .73 80 3070 7940 110 118 247 255 -100 488 181 307 .647 293 112 1.546 .879 -.629 -.187
10 487 338 112 123 375 215 452 326 158 182 340 203 0 0 224 150 303 306 56 18 9 3 590 543 1.744 .573 .597 .531 .557 1.804 32 143 .558 .8 60 3210 7920 109 115 262 268 -100 490 178 312 .831 472 294 1.203 .865 -.267 -.209
11 1497 2490 113 122 1384 2368 1131 1851 115 126 1018 1729 0 0 1038 1754 25 33 100 100 100 100 3752 2747 .584 1.711 1.698 1.719 1.767 1.415 32 182 1.725 .96 70 3340 7920 108 115 274 281 -100 3609 177 3432 2.48 2683 2506 .403 2.461 1.31 1.3
12 376 249 111 123 265 126 136 147 118 128 25 24 0 0 570 255 53 39 33 36 26 26 391 49 2.103 .475 .96 .839 .778 3.235 80 383 .43 .89 100 3460 7920 107 117 285 295 -50 361 178 183 .689 213 35 1.451 1.391 -.537 .476
13 570 565 109 125 461 440 508 525 111 128 399 400 0 0 312 276 22 33 100 100 100 96 901 799 1.048 .954 1.003 .982 .963 1.655 32 204 .949 .92 70 3620 7930 109 116 302 309 0 819 181 638 1.383 761 580 .723 1.453 .468 .539
14 1838 695 111 125 1727 570 1817 704 113 129 1706 579 0 0 475 210 21 31 100 100 100 100 2297 2285 3.03 .33 .339 .312 .343 1.424 32 206 .329 .95 70 3740 7930 109 116 314 321 0 1007 181 826 .478 1020 839 2.091 .492 -1.064 -1.024
15 982 548 111 118 871 430 844 508 114 120 733 390 0 0 551 227 23 32 100 100 100 100 1301 1123 2.026 .494 .532 .524 .553 1.383 12 104 .627 .92 50 3880 7920 109 114 329 334 0 794 171 623 .715 736 565 1.398 .771 -.483 -.375
16 2370 1117 112 122 2258 995 2478 1198 115 127 2366 1076 0 0 847 375 27 36 100 100 100 100 3253 3442 2.269 .441 .455 .428 .437 1.449 32 222 .399 .92 70 4010 7930 109 116 341 348 0 1619 177 1442 .639 1736 1559 1.566 .659 -.647 -.601
17 527 466 114 120 413 346 450 437 114 125 336 317 0 0 209 215 21 33 100 100 100 96 759 653 1.194 .838 .943 .795 .774 1.563 32 166 .873 .89 60 4160 7930 110 116 357 363 0 675 174 501 1.214 633 459 .824 1.367 .28 .451
18 848 301 114 126 734 175 834 316 115 128 720 190 0 0 408 112 21 30 100 82 100 78 909 910 4.194 .238 .264 .231 .253 1.935 52 263 .237 .91 80 4300 7920 108 116 370 378 0 436 183 254 .346 458 275 2.894 .382 -1.533 -1.387
19 558 297 113 128 445 169 556 298 114 129 443 170 0 0 157 93 18 33 100 90 100 87 614 613 2.633 .38 .384 .331 .371 1.958 32 198 .415 .87 70 4430 7920 108 115 383 390 0 430 186 245 .55 432 246 1.817 .556 -.861 -.846
20 1220 902 111 127 1109 775 1056 839 113 130 945 712 0 0 781 477 20 34 98 100 96 100 1884 1657 1.431 .699 .753 .827 .712 2.01 52 265 .653 .94 80 4570 7930 109 117 397 405 0 1307 184 1123 1.013 1216 1032 .987 1.092 .018 .127

Total number of rows: 39168

Table truncated, full table size 8738 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap