NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84741 Query DataSets for GSM84741
Status Public on Nov 23, 2005
Title FL19 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 lymphochip (FL19)
Organism Homo sapiens
Characteristics Follicular lymphoma lymphochip (FL19)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21059.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
1 207 230 191 201 16 29 197 207 194 208 6 6 0 0 57 82 45 71 28 26 7 10 45 12 .552 1.813 1 1.029 1.167 4.101 80 415 21.735 .03 100 1960 8790 86 96 75 85 -50 288 251 36 2.266 259 8 .441 1.25 1.18 .322
2 225 246 188 212 37 34 219 234 195 215 31 22 0 0 72 114 48 75 42 23 15 11 71 53 1.088 .919 .71 1.473 1.361 4.049 80 374 -1 -1 100 2120 8790 86 96 91 101 -50 308 265 43 1.149 293 28 .871 .887 .2 -.173
3 747 665 197 213 550 452 745 620 202 218 548 407 0 0 259 243 49 74 95 97 93 87 1002 955 1.217 .822 .743 .782 .769 2.207 80 404 .817 .75 110 2280 8800 86 97 106 117 0 831 266 565 1.027 775 509 .973 .928 .039 -.107
4 1160 613 192 214 968 399 1243 628 197 219 1051 414 0 0 452 225 51 74 91 88 90 85 1367 1465 2.426 .412 .394 .421 .389 2.657 80 395 .38 .73 110 2440 8810 87 98 122 133 0 766 268 499 .515 785 518 1.941 .492 -.957 -1.022
5 443 324 192 202 251 122 452 302 206 213 260 100 0 0 140 120 77 81 88 63 76 30 373 360 2.057 .486 .385 .538 .463 2.815 52 308 .411 .43 90 2590 8790 86 95 138 147 0 405 253 153 .608 378 125 1.646 .481 -.719 -1.057
6 7152 2429 195 211 6957 2218 8558 2700 211 219 8363 2489 0 0 4066 1089 125 80 91 93 85 92 9175 10852 3.137 .319 .298 .409 .307 4.693 120 471 .25 .8 120 2750 8800 86 98 153 165 0 3036 264 2773 .399 3375 3111 2.509 .372 -1.327 -1.427
7 388 283 176 207 212 76 393 275 188 219 217 68 0 0 134 98 58 80 86 42 76 13 288 285 2.789 .358 .313 .403 .447 3.166 52 268 .397 .26 90 2890 8810 88 97 168 177 0 354 259 95 .448 344 85 2.232 .392 -1.158 -1.352
8 158 217 161 198 -3 19 154 200 166 210 -7 2 0 0 47 79 45 79 11 21 1 5 16 -5 null null null 1.745 1.714 4.378 80 435 20.853 .05 100 3060 8790 86 96 185 195 -50 271 248 24 null 250 3 null null null null
9 243 260 151 196 92 64 248 254 158 205 97 58 0 0 97 90 46 66 73 46 53 25 156 155 1.438 .696 .598 .915 .851 3.623 52 251 2.426 .09 80 3220 8800 88 96 202 210 -100 325 245 80 .87 318 73 1.15 .747 -.202 -.42
10 160 219 157 201 3 18 153 209 162 206 -4 8 0 0 48 79 45 70 15 21 3 7 21 4 .167 6 null 1.302 1.696 5.399 80 417 18.105 .04 100 3370 8790 86 96 216 226 -100 274 251 23 7.5 261 10 .133 null 2.907 null
11 336 239 164 204 172 35 334 246 172 210 170 42 0 0 126 72 88 73 80 28 47 5 207 212 4.914 .203 .247 .398 .377 2.525 80 452 .251 .2 100 3550 8800 87 97 234 244 -100 299 255 44 .254 308 53 3.931 .309 -1.975 -1.695
12 321 237 162 200 159 37 308 229 174 207 146 29 0 0 123 86 111 79 71 26 30 11 196 175 4.297 .233 .199 .389 .424 3.3 52 316 .09 .11 90 3710 8780 85 94 250 259 -100 296 250 46 .291 286 36 3.438 .248 -1.782 -2.01
13 320 270 157 208 163 62 308 264 173 211 151 56 0 0 121 82 78 72 78 46 46 19 225 207 2.629 .38 .371 .702 .755 3.75 52 340 .174 .14 90 3840 8790 86 95 263 272 -100 338 260 78 .475 330 70 2.103 .464 -1.073 -1.109
14 708 379 161 199 547 180 738 341 168 206 577 142 0 0 266 153 53 67 92 75 91 55 727 719 3.039 .329 .246 .288 .301 3.3 80 478 .264 .5 110 4020 8790 85 96 280 291 0 474 249 225 .411 426 178 2.431 .308 -1.282 -1.701
15 279 266 159 207 120 59 274 259 168 210 115 52 0 0 112 94 51 67 75 38 51 21 179 167 2.034 .492 .452 .724 .703 4.826 52 310 .756 .13 90 4160 8790 86 95 295 304 0 333 259 74 .615 324 65 1.627 .565 -.702 -.823
16 544 407 158 208 386 199 523 401 162 208 365 193 0 0 194 138 43 68 97 83 96 61 585 558 1.94 .516 .529 .483 .531 2.299 80 429 .5 .56 110 4330 8790 85 96 311 322 0 509 260 249 .644 501 241 1.552 .661 -.634 -.597
17 166 202 164 210 2 -8 163 186 172 219 -1 -24 0 0 50 70 58 75 15 12 1 5 -6 -25 null null null 1.447 1.714 4.465 80 366 2.78 .16 100 4470 8780 85 95 326 336 -50 253 263 -10 null 233 null null null null null
18 467 264 171 208 296 56 470 251 183 217 299 43 0 0 165 87 63 77 91 36 90 13 352 342 5.286 .189 .144 .194 .254 3.197 80 412 .162 .23 110 4620 8800 86 97 340 351 0 330 260 70 .236 314 54 4.229 .18 -2.08 -2.476
19 210 228 180 210 30 18 212 220 184 215 32 10 0 0 55 76 47 71 35 25 11 7 48 42 1.667 .6 .313 1.637 1.614 3.065 80 396 -1 -1 100 4780 8780 85 95 357 367 -50 285 263 23 .75 275 13 1.333 .391 -.415 -1.356
20 531 286 171 210 360 76 518 288 174 212 347 78 0 0 208 97 42 68 88 55 86 27 436 425 4.737 .211 .225 .255 .249 2.715 80 370 .131 .26 100 4940 8790 86 96 373 383 0 358 263 95 .264 360 98 3.789 .281 -1.922 -1.831

Total number of rows: 37632

Table truncated, full table size 8128 Kbytes.




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