NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84715 Query DataSets for GSM84715
Status Public on Nov 23, 2005
Title FL7b 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 (FL7)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL7)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14685.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
1 495 1252 126 202 369 1050 491 1193 130 206 365 991 0 0 116 228 33 54 100 100 100 100 1419 1356 .351 2.846 2.715 2.925 2.8 1.281 32 187 2.952 .93 70 1860 8050 65 72 62 69 0 1490 240 1250 3.388 1420 1180 .295 3.232 1.76 1.693
2 172 296 115 219 57 77 131 252 119 224 16 33 0 0 153 167 36 54 25 40 16 23 134 49 .74 1.351 2.063 1.512 1.625 2.867 80 416 1.303 .75 100 1980 8030 62 72 73 83 -50 352 261 92 1.608 300 39 .622 2.455 .685 1.296
3 2655 1968 108 222 2547 1746 2836 1774 116 230 2728 1552 0 0 1144 807 44 55 100 100 100 100 4293 4280 1.459 .686 .569 .683 .69 1.304 32 174 .684 .97 70 2130 8040 64 71 89 96 0 2343 264 2079 .816 2112 1848 1.225 .677 -.293 -.562
4 135 244 110 215 25 29 106 216 118 220 -4 1 0 0 89 105 50 67 18 21 10 11 54 -3 .862 1.16 null 1.71 1.36 3.092 80 423 1.314 .77 100 2250 8030 62 72 100 110 -50 290 256 35 1.381 257 1 .724 null .466 null
5 1047 918 115 216 932 702 1148 872 121 221 1033 656 0 0 451 322 31 47 100 100 100 100 1634 1689 1.328 .753 .635 .761 .717 1.355 32 177 .738 .96 70 2420 8040 64 71 118 125 0 1093 257 836 .897 1038 781 1.115 .756 -.157 -.404
6 152 264 114 216 38 48 117 228 122 221 3 12 0 0 125 140 50 51 18 27 11 16 86 15 .792 1.263 4 1.982 1.626 3.859 80 423 1.367 .75 100 2520 8030 62 72 127 137 -50 314 257 57 1.504 271 14 .665 4.762 .589 2.252
7 852 962 113 218 739 744 611 784 118 219 498 566 0 0 432 501 24 47 100 100 100 100 1483 1064 .993 1.007 1.137 .926 .945 1.409 32 221 1.063 .94 70 2680 8040 64 71 144 151 0 1145 260 886 1.199 933 674 .834 1.353 .261 .436
8 726 713 115 229 611 484 728 681 121 239 613 452 0 0 300 216 34 66 100 100 100 100 1095 1065 1.262 .792 .737 .83 .759 1.316 12 104 .834 .94 50 2820 8030 64 69 159 164 0 849 273 576 .943 811 538 1.06 .878 -.085 -.188
9 466 474 108 214 358 260 386 413 114 216 278 199 0 0 343 173 48 50 91 91 83 91 618 477 1.377 .726 .716 .747 .938 2.076 12 104 .592 .78 50 2940 8040 65 70 171 176 0 564 255 310 .865 492 237 1.157 .852 -.21 -.231
10 314 524 108 205 206 319 279 528 110 209 171 323 0 0 126 153 23 47 100 93 96 90 525 494 .646 1.549 1.889 1.399 1.888 2.944 32 168 1.574 .82 60 3080 8040 65 71 185 191 0 624 244 380 1.844 629 385 .542 2.249 .882 1.169
11 914 3530 119 226 795 3304 655 2731 123 231 536 2505 0 0 707 2599 29 67 100 100 100 100 4099 3041 .241 4.156 4.674 4.648 4.38 1.414 32 152 3.987 .98 60 3210 8040 65 71 198 204 0 4202 269 3933 4.948 3251 2982 .202 5.564 2.307 2.476
12 194 324 123 229 71 95 126 236 125 237 3 7 0 0 189 206 26 89 28 28 23 21 166 10 .747 1.338 2.333 1.432 1.35 2.819 80 412 1.251 .83 100 3340 8030 62 72 209 219 -50 386 273 113 1.593 281 8 .628 2.778 .672 1.474
13 439 663 122 227 317 436 466 585 127 231 344 358 0 0 183 227 27 57 100 100 100 96 753 702 .727 1.375 1.041 1.474 1.349 1.539 32 157 1.407 .9 60 3490 8040 65 71 226 232 0 789 270 519 1.637 696 426 .611 1.239 .711 .309
14 1439 1504 121 224 1318 1280 1538 1266 129 258 1417 1042 0 0 410 1096 32 207 100 93 100 87 2598 2459 1.03 .971 .735 .791 .82 1.691 32 139 1.382 .77 60 3620 8040 65 71 239 245 0 1790 267 1524 1.156 1507 1240 .865 .875 .209 -.192
15 189 320 121 228 68 92 119 257 258 539 -2 29 0 0 180 191 1260 2579 0 0 0 0 160 27 .739 1.353 null 1.711 1.756 3.743 80 367 4.844 .51 100 3740 8030 62 72 249 259 -50 381 271 110 1.611 306 35 .621 null .688 null
16 2136 1999 114 227 2022 1772 2166 2019 117 228 2052 1792 0 0 476 368 31 57 100 100 100 100 3794 3844 1.141 .876 .873 .901 .874 1.311 32 181 .858 .97 70 3900 8040 64 71 266 273 0 2380 270 2110 1.043 2404 2133 .959 1.04 .061 .056
17 271 426 112 237 159 189 138 298 126 265 26 61 0 0 256 300 146 227 31 27 22 16 348 87 .841 1.189 2.346 1.301 1.105 2.7 80 402 1.276 .89 100 4020 8030 62 72 277 287 -50 507 282 225 1.415 355 73 .707 2.793 .501 1.482
18 814 548 110 216 704 332 816 560 113 233 706 344 0 0 210 161 26 100 100 90 100 75 1036 1050 2.12 .472 .487 .409 .447 1.764 32 166 .472 .83 60 4170 8030 64 70 294 300 0 652 257 395 .561 667 410 1.781 .58 -.833 -.786
19 463 557 103 213 360 344 473 528 118 261 370 315 0 0 142 125 91 348 96 43 90 0 704 685 1.047 .956 .851 .996 .988 1.629 32 168 1.033 .81 60 4300 8040 65 71 307 313 0 663 254 410 1.138 629 375 .879 1.014 .186 .019
20 1117 1575 110 225 1007 1350 1042 1391 121 264 932 1166 0 0 690 810 77 314 93 93 90 75 2357 2098 .746 1.341 1.251 1.458 1.302 1.621 32 206 1.289 .96 70 4430 8040 64 71 319 326 0 1875 268 1607 1.596 1656 1388 .627 1.489 .674 .575

Total number of rows: 39168

Table truncated, full table size 8470 Kbytes.




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