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Sample GSM84737 Query DataSets for GSM84737
Status Public on Nov 23, 2005
Title FL13.2 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 lymphochip (FL13.2)
Organism Homo sapiens
Characteristics Follicular lymphoma lymphochip (FL13.2)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21060.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
1 155 109 139 94 16 15 145 97 141 97 6 3 0 0 51 43 34 30 25 26 13 12 31 9 1.067 .938 .5 .89 1 5.228 80 422 .275 .1 100 1910 8890 80 90 78 88 -50 67 58 9 .579 60 2 1.728 .309 -.789 -1.696
2 147 101 145 97 2 4 155 98 207 206 10 1 0 0 35 30 665 846 0 0 0 0 6 11 .5 2 .1 .897 1.037 3.26 80 373 1.101 .05 100 2060 8890 80 90 93 103 -50 62 60 2 1.235 60 1 .81 .062 .304 -4.018
3 765 1364 153 102 612 1262 767 1392 213 208 614 1290 0 0 296 507 652 831 47 81 0 23 1874 1904 .485 2.062 2.101 2.41 2.18 1.983 80 387 1.611 .92 100 2220 8900 81 91 109 119 0 842 63 779 1.273 859 796 .786 1.297 .348 .375
4 1208 1086 154 100 1054 986 1272 1121 156 104 1118 1021 0 0 422 385 36 32 96 97 96 97 2040 2139 1.069 .935 .913 .946 .946 1.376 80 427 .909 .95 110 2390 8900 80 91 125 136 0 670 62 609 .577 692 630 1.732 .564 -.792 -.827
5 397 341 151 95 246 246 406 328 154 100 255 233 0 0 130 147 39 31 92 97 88 93 492 488 1 1 .914 .89 .912 1.874 80 330 1.017 .77 100 2540 8900 81 91 141 151 0 210 59 152 .617 202 144 1.62 .564 -.696 -.826
6 7292 3326 146 98 7146 3228 7709 3443 150 102 7563 3345 0 0 2601 1087 38 32 97 100 97 98 10374 10908 2.214 .452 .442 .498 .456 1.792 80 386 .44 .99 110 2690 8900 80 91 155 166 0 2053 60 1993 .279 2125 2065 3.586 .273 -1.842 -1.873
7 362 247 141 99 221 148 340 238 144 103 199 139 0 0 155 91 33 33 88 91 83 80 369 338 1.493 .67 .698 .652 .681 2.035 80 342 .586 .8 100 2850 8900 81 91 172 182 0 152 61 91 .413 147 86 2.419 .431 -1.274 -1.214
8 188 182 143 99 45 83 152 107 146 103 9 8 0 0 128 260 36 32 30 23 16 15 128 17 .542 1.844 .889 1.134 1.125 3.143 80 373 2.085 .83 100 3000 8890 80 90 187 197 -50 112 61 51 1.139 66 5 .878 .549 .187 -.866
9 217 243 145 99 72 144 234 246 151 102 89 147 0 0 74 79 45 32 70 91 47 82 216 236 .5 2 1.652 1.469 1.496 2.502 80 401 1.673 .55 110 3160 8900 80 91 202 213 0 150 61 89 1.235 152 91 .81 1.02 .304 .028
10 151 123 149 102 2 21 148 116 156 108 -1 14 0 0 40 50 69 65 7 12 0 3 23 13 .095 10.5 null 1.005 .692 4.866 80 382 .755 .18 100 3310 8880 79 89 218 228 -50 76 63 13 6.481 72 9 .154 null 2.696 null
11 348 261 150 102 198 159 343 254 155 106 193 152 0 0 117 85 70 33 88 95 77 87 357 345 1.245 .803 .788 .776 .734 2.007 80 424 .721 .75 110 3470 8890 79 90 233 244 0 161 63 98 .496 157 94 2.017 .486 -1.012 -1.041
12 167 140 154 105 13 35 147 114 156 109 -7 9 0 0 108 103 42 43 13 23 6 15 48 2 .371 2.692 null 1.102 .92 3.75 80 410 .947 .68 100 3620 8880 79 89 249 259 -50 86 65 22 1.662 70 6 .602 null .733 null
13 347 317 157 106 190 211 344 312 161 113 187 206 0 0 122 115 38 38 88 92 87 90 401 393 .9 1.111 1.102 1.055 1.093 2.342 80 366 1.023 .79 100 3790 8890 80 90 266 276 0 196 65 130 .686 193 127 1.459 .68 -.545 -.556
14 218 244 168 118 50 126 165 133 172 125 -3 15 0 0 193 355 44 42 21 33 11 17 176 12 .397 2.52 null 1.242 1.597 5.435 80 352 1.944 .89 100 3930 8880 79 89 280 290 -50 151 73 78 1.556 82 9 .643 null .637 null
15 310 316 174 123 136 193 318 322 183 127 144 199 0 0 101 96 53 43 80 92 70 88 329 343 .705 1.419 1.382 1.454 1.257 2.331 80 370 1.275 .68 100 4090 8890 80 90 296 306 0 195 76 119 .876 199 123 1.142 .853 -.191 -.229
16 584 1579 187 128 397 1451 613 1631 197 135 426 1503 0 0 188 487 71 49 95 100 90 100 1848 1929 .274 3.655 3.528 3.839 3.75 1.459 80 404 3.596 .92 110 4250 8890 79 90 311 322 0 975 79 896 2.256 1007 928 .443 2.178 1.174 1.123
17 178 118 190 131 -12 -13 176 113 207 140 -14 -18 0 0 48 33 100 53 1 1 0 0 -25 -32 null null null .713 .617 4.45 80 380 .263 .25 100 4400 8880 79 89 327 337 -50 73 81 -8 null 70 null null null null null
18 567 283 173 112 394 171 579 269 179 117 406 157 0 0 123 95 56 39 98 92 98 86 565 563 2.304 .434 .387 .385 .414 1.905 80 398 .407 .8 110 4560 8890 79 90 342 353 0 175 69 106 .268 166 97 3.733 .239 -1.9 -2.067
19 166 118 164 105 2 13 165 109 166 108 1 4 0 0 44 49 42 34 18 25 2 10 15 5 .154 6.5 4 1.02 1.093 5.635 80 350 .617 .16 100 4710 8880 79 89 358 368 -50 73 65 8 4.012 67 2 .249 2.469 2.004 1.304
20 553 308 154 108 399 200 578 296 159 110 424 188 0 0 197 125 42 35 88 92 88 87 599 612 1.995 .501 .443 .504 .468 2.208 80 395 .457 .78 110 4860 8890 79 90 372 383 0 190 67 123 .309 183 116 3.232 .274 -1.692 -1.869

Total number of rows: 37632

Table truncated, full table size 8207 Kbytes.




Supplementary data files not provided
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