NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84723 Query DataSets for GSM84723
Status Public on Nov 23, 2005
Title FL2 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 lymphochip (FL2)
Organism Homo sapiens
Characteristics Follicular lymphoma lymphochip (FL2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18863.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 90 60 74 53 16 7 84 57 77 56 10 4 0 0 32 19 36 22 17 17 5 5 23 14 2.286 .438 .4 .734 1 3.839 80 416 .338 .27 100 1520 9280 59 69 47 57 -50 82 73 10 .599 78 5 1.669 .548 -.739 -.868
2 83 65 73 55 10 10 82 61 73 57 9 6 0 0 29 21 27 20 26 22 6 8 20 15 1 1 .667 .535 .564 2.804 80 392 .292 .22 100 1680 9280 59 69 63 73 -50 89 75 14 1.37 84 8 .73 .913 .454 -.131
3 1047 950 77 56 970 894 1115 1005 120 82 1038 949 0 0 387 351 193 102 96 98 90 96 1864 1987 1.085 .922 .914 .941 .917 1.616 80 411 .854 .9 110 1850 9290 59 70 79 90 0 1301 77 1225 1.263 1377 1300 .792 1.252 .336 .325
4 1936 809 77 55 1859 754 2158 873 123 85 2081 818 0 0 722 327 199 105 92 91 90 88 2613 2899 2.466 .406 .393 .414 .41 1.745 80 383 .391 .92 110 2000 9290 59 70 94 105 0 1108 75 1033 .556 1196 1121 1.8 .538 -.848 -.893
5 405 239 73 52 332 187 414 227 77 57 341 175 0 0 156 86 24 24 96 97 96 93 519 516 1.775 .563 .513 .571 .543 2.181 80 355 .478 .79 100 2150 9290 60 70 110 120 0 327 71 256 .772 311 240 1.296 .703 -.374 -.508
6 8764 2115 74 52 8690 2063 9620 2287 79 55 9546 2235 0 0 3161 687 34 22 100 100 100 100 10753 11781 4.212 .237 .234 .252 .229 1.829 80 402 .211 .92 110 2310 9290 59 70 125 136 0 2897 71 2826 .325 3133 3062 3.075 .321 -1.621 -1.641
7 377 180 77 57 300 123 387 184 100 70 310 127 0 0 177 74 106 61 83 76 65 52 423 437 2.439 .41 .41 .396 .406 1.997 80 342 .412 .83 100 2470 9290 60 70 142 152 0 247 78 168 .562 252 174 1.78 .561 -.832 -.833
8 81 56 82 54 -1 2 78 53 102 68 -4 -1 0 0 22 25 99 61 0 1 0 0 1 -5 null null null 1.312 1.264 3.595 80 364 .604 .82 100 2610 9280 59 69 156 166 -50 77 74 3 null 73 null null null null null
9 221 267 82 57 139 210 223 260 85 59 141 203 0 0 95 107 22 21 88 97 87 93 349 344 .662 1.511 1.44 1.61 1.516 2.337 80 398 1.381 .77 110 2780 9290 59 70 172 183 0 366 78 288 2.07 356 278 .483 1.972 1.049 .98
10 81 64 82 59 -1 5 77 59 86 61 -5 0 0 0 22 22 27 22 13 20 0 3 4 -5 null null null .594 .5 3.281 80 364 .159 .09 100 2920 9280 59 69 187 197 -50 88 81 7 null 81 0 null null null null
11 249 191 83 55 166 136 249 181 86 58 166 126 0 0 115 88 27 22 87 91 77 82 302 292 1.221 .819 .759 .828 .864 2.477 80 424 .729 .71 110 3090 9280 58 69 203 214 0 262 75 186 1.122 248 173 .891 1.04 .166 .056
12 98 83 84 58 14 25 77 61 88 61 -7 3 0 0 71 79 32 21 21 30 15 16 39 -4 .56 1.786 null .546 .526 3.827 80 364 .649 .4 100 3240 9280 59 69 219 229 -100 114 79 34 2.446 84 4 .409 null 1.291 null
13 197 177 84 58 113 119 106 130 88 60 22 72 0 0 183 161 30 20 47 60 43 58 232 94 .95 1.053 3.273 .771 .742 2.711 80 357 .809 .8 100 3410 9290 60 70 236 246 -100 242 79 163 1.443 178 99 .693 4.483 .529 2.165
14 115 102 85 57 30 45 87 71 89 59 2 14 0 0 101 94 24 21 31 45 18 28 75 16 .667 1.5 7 .824 1.067 5.964 80 354 .82 .18 100 3550 9280 59 69 250 260 -100 140 78 62 2.055 97 19 .487 9.589 1.039 3.261
15 306 254 85 59 221 195 337 259 87 61 252 200 0 0 145 105 22 22 86 96 80 90 416 452 1.133 .882 .794 .932 .89 2.15 80 372 .774 .84 100 3710 9290 60 70 266 276 -100 348 81 267 1.209 355 274 .827 1.087 .273 .121
16 821 1098 83 54 738 1044 909 1177 85 59 826 1123 0 0 384 440 24 22 92 98 91 98 1782 1949 .707 1.415 1.36 1.655 1.457 1.834 80 365 1.35 .93 100 3870 9280 59 69 282 292 0 1504 74 1430 1.938 1612 1538 .516 1.862 .954 .897
17 84 71 79 56 5 15 79 64 82 60 0 8 0 0 27 28 25 22 20 31 7 13 20 8 .333 3 null .973 .727 5.719 80 351 1.598 .06 100 4020 9280 59 69 297 307 -50 97 77 21 4.11 88 11 .243 null 2.039 null
18 254 147 79 59 175 88 259 143 82 62 180 84 0 0 90 57 25 22 88 88 87 73 263 264 1.989 .503 .467 .558 .518 2.324 80 366 .458 .72 100 4170 9270 58 68 312 322 0 201 81 121 .689 196 115 1.452 .639 -.538 -.646
19 68 59 81 58 -13 1 63 56 84 62 -18 -2 0 0 30 22 25 22 5 17 2 1 -12 -20 null null null .834 .719 3.023 80 363 .185 .08 100 4330 9280 59 69 328 338 -50 81 79 1 null 77 null null null null null
20 428 306 81 62 347 244 430 288 85 66 349 226 0 0 196 139 25 24 90 93 90 92 591 575 1.422 .703 .648 .701 .667 1.994 80 344 .653 .86 100 4490 9290 60 70 344 354 0 419 85 334 .963 395 310 1.038 .887 -.054 -.173

Total number of rows: 37632

Table truncated, full table size 7936 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap