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Sample GSM84738 Query DataSets for GSM84738
Status Public on Nov 23, 2005
Title FL1 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 (FL1)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21061.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
1 133 147 129 137 4 10 128 139 135 143 -1 2 0 0 48 48 45 44 13 20 1 6 14 1 .4 2.5 null .866 .886 5.179 80 416 -1 -1 100 1450 8560 51 61 72 82 -50 128 119 9 2.174 121 2 .46 null 1.12 null
2 130 139 124 138 6 1 126 136 130 144 2 -2 0 0 38 40 43 47 12 15 3 1 7 0 6 .167 null 1.089 .929 5.369 80 387 .631 .04 100 1610 8560 51 61 88 98 -50 121 120 1 .145 118 null 6.9 null -2.787 null
3 603 690 126 136 477 554 472 550 132 141 346 414 0 0 365 415 43 48 94 96 91 91 1031 760 .861 1.161 1.197 1.185 1.145 2.093 156 760 1.152 .91 150 1800 8560 48 63 104 119 -100 600 118 482 1.01 478 360 .99 1.04 .014 .057
4 2409 986 128 133 2281 853 2592 1017 134 140 2464 884 0 0 731 239 40 54 100 100 100 100 3134 3348 2.674 .374 .359 .39 .369 1.445 80 333 .356 .94 110 1930 8570 51 62 119 130 0 857 116 742 .325 884 769 3.075 .312 -1.621 -1.681
5 367 282 133 137 234 145 362 278 137 145 229 141 0 0 134 75 41 52 93 87 88 73 379 370 1.614 .62 .616 .596 .689 2.307 80 359 .532 .65 100 2080 8570 52 62 135 145 0 245 119 126 .539 242 123 1.856 .535 -.892 -.901
6 12740 3302 132 135 12608 3167 14281 3516 135 140 14149 3381 0 0 4106 811 41 47 100 100 100 100 15775 17530 3.981 .251 .239 .26 .248 1.289 80 368 .235 .96 100 2240 8570 52 62 151 161 0 2871 117 2754 .218 3057 2940 4.578 .208 -2.195 -2.267
7 545 286 128 137 417 149 533 277 130 142 405 140 0 0 187 68 37 46 98 96 98 82 566 545 2.799 .357 .346 .375 .367 2.62 52 300 .279 .63 90 2390 8570 52 61 166 175 0 249 119 130 .311 241 122 3.218 .301 -1.686 -1.734
8 160 179 131 142 29 37 146 159 136 147 15 17 0 0 83 98 44 49 18 26 11 21 66 32 .784 1.276 1.133 1.358 1.11 3.335 80 396 1.557 .48 100 2550 8560 51 61 182 192 -50 156 123 32 1.109 138 15 .901 .986 .15 -.021
9 568 746 131 144 437 602 532 537 143 152 401 393 0 0 264 551 55 53 98 100 96 98 1039 794 .726 1.378 .98 1.203 1.236 1.876 52 312 1.784 .79 90 2700 8560 51 60 197 206 -100 649 125 523 1.198 467 342 .835 .852 .26 -.231
10 213 224 124 143 89 81 155 212 141 159 31 69 0 0 150 97 83 80 30 45 21 13 170 100 1.099 .91 2.226 1.045 .833 3.927 80 366 .659 .57 100 2860 8560 51 61 213 223 -100 195 124 70 .791 184 60 1.264 1.935 -.338 .953
11 413 345 128 144 285 201 411 312 143 161 283 168 0 0 154 144 85 75 90 88 78 58 486 451 1.418 .705 .594 .684 .653 2.055 80 328 .831 .79 100 3010 8560 51 61 228 238 -50 300 125 175 .613 271 146 1.631 .516 -.705 -.954
12 137 163 127 142 10 21 136 152 132 149 9 10 0 0 45 64 39 48 20 23 5 11 31 19 .476 2.1 1.111 1.403 1.188 3.998 80 359 5.441 .15 100 3170 8560 51 61 244 254 -50 142 123 18 1.826 132 9 .548 .966 .869 -.05
13 277 240 126 139 151 101 277 236 132 144 151 97 0 0 79 75 40 52 93 75 81 47 252 248 1.495 .669 .642 .622 .721 2.905 80 356 .721 .49 100 3330 8570 52 62 260 270 0 209 121 88 .582 205 84 1.719 .559 -.782 -.84
14 134 163 131 137 3 26 128 151 136 145 -3 14 0 0 38 72 39 54 15 22 3 11 29 11 .115 8.667 null 1.737 1.5 4.915 80 393 -1 -1 100 3480 8550 50 60 275 285 -50 142 119 23 7.536 131 12 .133 null 2.914 null
15 305 283 125 143 180 140 279 292 132 148 154 149 0 0 90 80 40 51 96 82 92 67 320 303 1.286 .778 .968 .765 .905 2.259 52 331 .807 .61 90 3650 8570 52 61 292 301 -100 246 124 122 .676 254 130 1.479 .841 -.564 -.249
16 513 679 126 143 387 536 514 678 135 182 388 535 0 0 207 226 47 313 92 87 90 30 923 923 .722 1.385 1.379 1.633 1.345 2.03 80 450 1.363 .87 110 3830 8550 49 60 309 320 -100 590 124 466 1.204 590 465 .83 1.199 .268 .262
17 130 138 120 131 10 7 124 131 130 154 4 0 0 0 45 46 44 234 20 0 5 0 17 4 1.429 .7 null .956 1.077 4.657 80 362 2.008 .09 100 3950 8550 50 60 322 332 -100 120 114 6 .609 114 0 1.643 null -.716 null
18 416 272 119 136 297 136 410 249 128 143 291 113 0 0 101 94 44 47 98 88 98 63 433 404 2.184 .458 .388 .416 .43 1.922 52 313 .404 .57 90 4110 8560 51 60 338 347 -100 237 118 118 .398 217 98 2.511 .338 -1.328 -1.566
19 127 154 127 139 0 15 121 151 133 144 -6 12 0 0 42 47 41 51 12 20 7 6 15 6 null null null .984 1.285 3.731 80 408 -1 -1 100 4260 8550 50 60 353 363 -100 134 121 13 null 131 10 null null null null
20 320 267 124 131 196 136 334 251 130 137 210 120 0 0 97 102 41 48 88 80 84 63 332 330 1.441 .694 .571 .745 .73 2.376 52 326 .711 .55 90 4430 8550 50 59 370 379 -100 232 114 118 .603 218 104 1.657 .497 -.729 -1.009

Total number of rows: 37632

Table truncated, full table size 8252 Kbytes.




Supplementary data files not provided
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