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Sample GSM84731 Query DataSets for GSM84731
Status Public on Nov 23, 2005
Title FL20 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 (FL20)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL20)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24614.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) [email protected]
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
1 146 116 134 76 12 40 141 96 138 78 7 20 0 0 51 87 36 21 18 45 6 25 52 27 .3 3.333 2.857 1.014 .667 4.649 80 424 6.358 .17 100 1670 8670 62 72 62 72 -50 112 73 38 3.205 92 19 .312 2.747 1.68 1.458
2 144 84 136 74 8 10 144 75 138 77 8 1 0 0 37 45 38 29 18 15 6 7 18 9 .8 1.25 .125 .784 .817 3.902 80 391 1.129 .2 100 1820 8670 62 72 77 87 -50 81 71 10 1.202 72 1 .832 .12 .265 -3.057
3 835 758 136 70 699 688 847 779 141 85 711 709 0 0 210 225 40 64 100 100 100 100 1387 1420 1.016 .984 .997 .979 .993 1.618 52 315 1.046 .87 90 1990 8670 62 71 94 103 0 729 67 662 .946 749 682 1.057 .959 -.079 -.061
4 1718 852 143 74 1575 778 1812 919 146 83 1669 845 0 0 579 307 40 46 100 100 100 98 2353 2514 2.024 .494 .506 .476 .483 1.641 80 371 .477 .91 100 2140 8680 63 73 109 119 0 819 71 748 .475 884 813 2.105 .487 -1.074 -1.039
5 401 236 143 73 258 163 413 219 145 76 270 146 0 0 117 88 35 23 97 93 95 93 421 416 1.583 .632 .541 .585 .595 2.149 80 358 .559 .73 100 2300 8680 63 73 125 135 0 227 70 157 .607 211 140 1.646 .52 -.719 -.944
6 7870 3296 140 76 7730 3220 8475 3776 142 78 8335 3700 0 0 2911 1304 36 30 100 100 100 100 10950 12035 2.401 .417 .444 .4 .413 1.563 80 373 .404 .91 100 2450 8680 63 73 140 150 0 3169 73 3096 .401 3631 3558 2.497 .427 -1.32 -1.228
7 423 189 136 74 287 115 418 181 137 77 282 107 0 0 130 59 36 32 96 96 94 76 402 389 2.496 .401 .379 .42 .372 2.394 52 301 .37 .79 90 2600 8680 63 72 155 164 0 182 71 111 .385 174 103 2.595 .365 -1.376 -1.455
8 142 135 132 74 10 61 140 79 136 76 8 5 0 0 32 159 35 22 21 28 5 20 71 13 .164 6.1 .625 1.893 1.974 6.315 80 421 17.756 .12 100 2760 8670 62 72 171 181 -50 130 71 59 5.865 76 5 .17 .601 2.552 -.735
9 219 141 137 78 82 63 210 141 140 80 73 63 0 0 68 39 37 21 82 84 48 69 145 136 1.302 .768 .863 .7 .747 2.367 52 314 .443 .42 90 2920 8690 64 73 187 196 0 136 75 61 .739 136 61 1.354 .83 -.437 -.269
10 142 158 143 81 -1 77 142 92 143 83 -1 11 0 0 34 176 37 25 11 35 2 26 76 10 null null null 1.396 1.813 5.009 80 409 22.399 .1 100 3080 8670 62 72 203 213 -50 152 78 74 null 88 11 null null null null
11 349 154 144 78 205 76 368 157 144 86 224 79 0 0 113 45 38 56 92 69 82 21 281 303 2.697 .371 .353 .461 .427 2.136 52 323 .312 .63 90 3230 8680 63 72 218 227 0 148 75 73 .356 151 76 2.805 .339 -1.488 -1.56
12 146 117 144 76 2 41 142 86 145 83 -2 10 0 0 36 80 38 51 16 23 1 17 43 8 .049 20.5 null 1.007 1.042 4.704 80 406 -1 -1 100 3390 8670 62 72 234 244 -50 113 73 39 19.712 83 10 .051 null 4.301 null
13 328 142 134 76 194 66 335 140 139 78 201 64 0 0 98 40 36 23 88 84 88 69 260 265 2.939 .34 .318 .343 .363 2.19 52 313 .281 .63 90 3550 8680 63 72 250 259 0 137 73 63 .327 135 62 3.057 .306 -1.612 -1.708
14 152 172 140 78 12 94 154 95 142 80 14 17 0 0 40 200 36 24 25 41 5 28 106 31 .128 7.833 1.214 1.389 1.343 5.567 80 408 16.987 .15 100 3700 8670 62 72 265 275 -50 165 75 90 7.532 91 16 .133 1.168 2.913 .224
15 362 166 138 80 224 86 359 163 142 82 221 83 0 0 114 42 33 23 94 94 90 82 310 304 2.605 .384 .376 .383 .417 2.247 52 301 .319 .68 90 3860 8680 63 72 281 290 0 160 77 83 .369 157 80 2.709 .361 -1.438 -1.469
16 220 292 143 82 77 210 165 105 164 106 22 23 0 0 143 454 117 118 25 28 13 22 287 45 .367 2.727 1.045 1.164 .938 3.606 80 395 3.483 .51 100 4010 8670 62 72 296 306 -100 281 79 202 2.622 101 22 .381 1.005 1.391 .008
17 140 110 147 78 -7 32 138 82 168 106 -9 4 0 0 40 87 118 120 1 8 0 7 25 -5 null null null .888 1.13 5.084 80 388 .928 .76 100 4170 8680 63 73 312 322 -50 106 75 31 null 79 4 null null null null
18 499 173 145 78 354 95 490 172 147 83 345 94 0 0 128 45 34 27 100 95 100 85 449 439 3.726 .268 .272 .265 .267 1.823 80 379 .189 .51 100 4340 8670 62 72 329 339 0 166 75 91 .258 165 90 3.875 .262 -1.954 -1.932
19 142 121 142 79 0 42 137 89 145 82 -5 10 0 0 41 103 36 26 16 33 7 17 42 5 null null null .676 .555 5.111 80 358 9.286 .1 100 4480 8680 63 73 343 353 -50 116 76 40 null 86 10 null null null null
20 192 201 138 75 54 126 168 140 140 77 30 65 0 0 83 178 34 24 46 67 35 55 180 95 .429 2.333 2.167 1.728 1.438 5.325 80 383 5.146 .25 100 4640 8680 63 73 359 369 -100 193 72 121 2.244 135 63 .446 2.083 1.166 1.059

Total number of rows: 37632

Table truncated, full table size 8169 Kbytes.




Supplementary data files not provided

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