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Sample GSM84736 Query DataSets for GSM84736
Status Public on Nov 23, 2005
Title FL16 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 (FL16)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL16)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24548.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
1 167 95 163 77 4 18 158 87 167 81 -5 10 0 0 51 42 40 23 16 30 6 15 22 5 .222 4.5 null .583 .5 5.17 80 437 -1 -1 100 2060 8540 65 75 77 87 -50 91 74 17 4.327 84 10 .231 null 2.113 null
2 167 84 165 80 2 4 167 80 171 82 2 0 0 0 44 23 46 20 16 20 2 6 6 2 .5 2 null .632 .541 3.565 80 379 51.026 .03 100 2220 8540 65 75 93 103 -50 81 77 4 1.923 77 0 .52 null .943 null
3 748 943 169 80 579 863 766 963 173 82 597 883 0 0 289 286 47 24 96 100 95 100 1442 1480 .671 1.491 1.479 1.677 1.546 1.683 80 450 1.392 .92 110 2380 8550 65 76 108 119 0 907 77 830 1.433 926 849 .698 1.422 .519 .508
4 1166 637 167 77 999 560 1149 639 173 83 982 562 0 0 263 127 45 27 100 100 100 100 1559 1544 1.784 .561 .572 .571 .55 1.366 80 419 .537 .93 110 2540 8550 65 76 124 135 0 613 74 538 .539 614 540 1.855 .55 -.892 -.862
5 425 242 163 75 262 167 435 238 169 81 272 163 0 0 119 74 45 26 96 100 88 95 429 435 1.569 .637 .599 .653 .634 1.842 80 382 .561 .79 110 2690 8550 65 76 139 150 0 233 72 161 .613 229 157 1.632 .576 -.706 -.795
6 5010 2736 159 75 4851 2661 5479 3083 162 78 5320 3008 0 0 2450 1041 42 20 98 100 96 100 7512 8328 1.823 .549 .565 .626 .541 1.706 120 433 .502 .95 120 2850 8560 66 78 155 167 0 2631 72 2559 .527 2964 2892 1.896 .544 -.923 -.879
7 373 188 161 77 212 111 368 184 173 79 207 107 0 0 135 59 89 22 78 95 57 88 323 314 1.91 .524 .517 .536 .53 1.948 80 303 .395 .76 100 3010 8560 67 77 172 182 0 181 74 107 .503 177 103 1.986 .497 -.99 -1.009
8 177 122 158 77 19 45 163 80 161 82 5 3 0 0 80 125 41 26 22 28 8 20 64 8 .422 2.368 .6 .783 .973 4.091 80 367 1.601 .58 100 3150 8540 65 75 186 196 -50 117 74 43 2.277 77 3 .439 .577 1.187 -.794
9 254 187 158 77 96 110 246 187 161 82 88 110 0 0 74 46 39 22 72 97 52 92 206 198 .873 1.146 1.25 1.227 1.206 2.343 80 344 .706 .54 100 3320 8560 67 77 203 213 0 180 74 106 1.102 180 106 .908 1.202 .14 .265
10 177 101 159 79 18 22 171 88 162 81 12 9 0 0 50 62 42 23 26 30 8 17 40 21 .818 1.222 .75 .723 .679 3.753 80 369 1.062 .19 100 3460 8540 65 75 217 227 -50 97 76 21 1.175 85 9 .851 .721 .233 -.472
11 348 179 153 77 195 102 350 178 158 80 197 101 0 0 88 47 40 24 95 95 91 87 297 298 1.912 .523 .513 .54 .516 2.231 80 383 .424 .69 100 3630 8550 66 76 234 244 0 172 74 98 .503 171 97 1.988 .493 -.991 -1.02
12 178 119 159 80 19 39 169 84 165 82 10 4 0 0 66 118 44 26 26 30 6 18 58 14 .487 2.053 .4 .9 .744 5.276 80 393 2.19 .35 100 3780 8540 65 75 249 259 -50 114 77 38 1.974 81 4 .507 .385 .981 -1.379
13 363 206 164 78 199 128 349 210 167 81 185 132 0 0 93 58 41 22 98 100 91 95 327 317 1.555 .643 .714 .655 .616 1.809 80 359 .562 .77 100 3940 8560 67 77 265 275 0 198 75 123 .618 202 127 1.617 .686 -.693 -.544
14 196 143 164 79 32 64 173 92 167 80 9 13 0 0 103 135 42 22 21 37 15 26 96 22 .5 2 1.444 1.197 1.198 4.025 80 381 1.322 .71 100 4090 8540 65 75 280 290 -50 138 76 62 1.923 88 13 .52 1.389 .943 .474
15 337 206 163 80 174 126 338 201 168 82 175 121 0 0 78 54 48 26 95 98 86 93 300 296 1.381 .724 .691 .724 .672 2.147 80 412 .634 .7 110 4260 8550 65 76 296 307 0 198 77 121 .696 193 116 1.436 .665 -.522 -.589
16 558 911 163 86 395 825 551 911 174 88 388 825 0 0 150 237 109 27 98 100 87 100 1220 1213 .479 2.089 2.126 2.193 2.084 1.625 80 346 2.156 .88 100 4410 8540 65 75 312 322 0 876 83 793 2.008 876 793 .498 2.045 1.006 1.032
17 184 98 163 85 21 13 180 97 168 87 17 12 0 0 58 28 42 24 26 25 10 10 34 29 1.615 .619 .706 .549 .568 3.338 80 359 .042 .04 100 4560 8540 65 75 327 337 -50 94 82 13 .595 93 12 1.68 .679 -.748 -.559
18 616 208 161 85 455 123 628 204 165 87 467 119 0 0 160 63 39 24 100 95 97 92 578 586 3.699 .27 .255 .256 .263 2.109 80 364 .214 .69 100 4720 8540 65 75 343 353 0 200 82 118 .26 196 114 3.847 .245 -1.944 -2.029
19 170 83 161 83 9 0 163 83 167 84 2 0 0 0 50 19 40 23 26 12 8 2 9 2 null null null .448 .391 5.049 80 365 .033 .05 100 4870 8540 65 75 358 368 -50 80 80 0 null 80 0 null null null null
20 686 264 159 83 527 181 683 265 166 86 524 182 0 0 153 71 43 26 100 97 100 96 708 706 2.912 .343 .347 .323 .343 1.822 80 424 .297 .76 110 5030 8550 65 76 373 384 0 254 80 174 .33 255 175 3.028 .334 -1.598 -1.582

Total number of rows: 37632

Table truncated, full table size 8070 Kbytes.




Supplementary data files not provided

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