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Sample GSM84735 Query DataSets for GSM84735
Status Public on Nov 23, 2005
Title FL24 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 (FL24)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL24)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, Follicular Lymphoma
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24903.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
1 167 225 147 213 20 12 158 214 154 223 11 1 0 0 62 70 45 77 23 16 7 3 32 12 1.667 .6 .091 1.054 1.445 5.094 80 414 20.898 .03 100 1800 8870 74 84 51 61 -50 227 215 12 .606 216 1 1.65 .092 -.722 -3.445
2 165 235 154 209 11 26 165 217 161 216 11 8 0 0 43 103 49 78 15 22 3 5 37 19 .423 2.364 .727 1.965 2.183 3.69 80 381 -1 -1 100 1960 8870 74 84 67 77 -50 237 211 26 2.388 219 8 .419 .735 1.256 -.445
3 894 1252 150 223 744 1029 886 1214 158 230 736 991 0 0 355 449 44 74 97 97 97 97 1773 1727 .723 1.383 1.346 1.418 1.361 1.52 80 387 1.387 .91 110 2110 8890 75 86 81 92 0 1265 225 1039 1.397 1226 1001 .716 1.36 .482 .444
4 2246 1292 154 228 2092 1064 2217 1272 158 236 2063 1044 0 0 761 464 43 72 98 96 97 96 3156 3107 1.966 .509 .506 .509 .503 1.381 80 370 .498 .93 100 2270 8880 75 85 98 108 0 1305 230 1075 .514 1285 1055 1.947 .511 -.961 -.968
5 337 386 145 215 192 171 340 367 148 226 195 152 0 0 106 162 40 76 92 71 91 48 363 347 1.123 .891 .779 .767 .795 2.768 80 358 1.255 .63 100 2430 8880 75 85 114 124 0 390 217 173 .9 371 154 1.112 .787 -.153 -.345
6 8488 3266 138 184 8350 3082 8795 3368 143 193 8657 3184 0 0 3374 1275 37 68 100 98 97 98 11432 11841 2.709 .369 .368 .415 .343 1.847 80 418 .346 .93 110 2580 8880 74 85 128 139 0 3299 186 3113 .373 3402 3216 2.682 .372 -1.423 -1.429
7 319 183 139 150 180 33 326 183 144 160 187 33 0 0 123 56 38 62 84 26 82 9 213 220 5.455 .183 .176 .252 .22 3.458 52 313 .088 .09 90 2740 8880 75 84 145 154 0 185 152 33 .185 185 33 5.4 .178 -2.433 -2.488
8 133 141 140 130 -7 11 129 120 142 136 -11 -10 0 0 39 67 39 48 12 20 2 10 4 -21 null null null 1.387 1.621 3.346 80 436 7.08 .08 100 2900 8870 74 84 161 171 -50 142 131 11 null 121 null null null null null
9 210 189 152 135 58 54 190 166 156 141 38 31 0 0 61 60 51 47 41 33 25 33 112 69 1.074 .931 .816 1.093 1.154 3.392 12 90 .865 .31 50 3050 8850 74 79 178 183 0 191 136 55 .94 168 31 1.063 .824 -.089 -.279
10 157 159 137 130 20 29 143 145 142 137 6 15 0 0 62 71 39 50 23 23 10 16 49 21 .69 1.45 2.5 1.499 1.574 5.618 80 435 2.426 .2 100 3210 8870 74 84 192 202 -50 161 131 29 1.465 146 15 .683 2.525 .551 1.336
11 263 181 140 123 123 58 250 167 143 131 110 44 0 0 97 58 38 49 82 44 63 26 181 154 2.121 .472 .4 .501 .449 2.726 52 313 .366 .33 90 3370 8880 75 84 208 217 0 183 124 59 .476 169 44 2.099 .404 -1.07 -1.307
12 145 165 143 138 2 27 134 144 146 150 -9 6 0 0 45 72 41 59 16 28 5 8 29 -3 .074 13.5 null 1.574 1.706 3.422 80 402 3.538 .2 100 3520 8870 74 84 223 233 -50 167 139 27 13.636 145 6 .073 null 3.769 null
13 266 174 140 133 126 41 251 167 145 140 111 34 0 0 113 56 44 53 78 34 61 11 167 145 3.073 .325 .306 .448 .351 4.362 52 256 .249 .32 80 3700 8880 76 84 242 250 0 176 134 41 .329 169 34 3.042 .309 -1.605 -1.692
14 140 140 135 128 5 12 134 125 139 134 -1 -3 0 0 48 64 38 50 17 15 6 8 17 -4 .417 2.4 null 1.401 1.261 3.723 80 404 7.811 .14 100 3830 8870 74 84 254 264 -50 141 129 12 2.424 126 null .413 null 1.278 null
15 223 171 137 114 86 57 228 177 139 121 91 63 0 0 70 49 40 43 78 59 53 25 143 154 1.509 .663 .692 .626 .741 2.591 52 328 .419 .3 90 4020 8880 75 84 273 282 0 173 115 58 .669 179 64 1.494 .699 -.579 -.516
16 506 712 141 121 365 591 515 689 144 128 374 568 0 0 153 249 42 47 97 98 96 98 956 942 .618 1.619 1.519 1.607 1.672 2 80 370 1.706 .85 100 4170 8870 74 84 288 298 0 719 122 597 1.636 696 574 .611 1.534 .71 .617
17 135 137 137 123 -2 14 132 126 140 129 -5 3 0 0 32 52 38 45 8 23 1 10 12 -2 null null null 1.253 1.197 3.663 80 367 2.642 .2 100 4300 8870 74 84 301 311 -50 138 124 14 null 127 3 null null null null
18 429 181 136 116 293 65 423 171 141 125 287 55 0 0 107 66 38 46 98 57 96 23 358 342 4.508 .222 .192 .212 .25 2.589 80 376 .224 .53 100 4480 8870 74 84 319 329 0 183 117 66 .224 173 56 4.463 .194 -2.158 -2.369
19 142 125 138 120 4 5 139 121 142 128 1 1 0 0 32 41 38 46 13 12 5 2 9 2 .8 1.25 1 1.53 2.1 6.266 80 338 3.855 .13 100 4620 8860 73 83 333 343 -50 126 121 5 1.263 122 1 .792 1.01 .336 .014
20 467 187 134 119 333 68 467 179 138 126 333 60 0 0 127 75 36 45 98 57 97 33 401 393 4.897 .204 .18 .199 .225 2.45 80 351 .176 .45 100 4770 8870 74 84 348 358 0 189 120 69 .206 181 61 4.848 .182 -2.277 -2.458

Total number of rows: 37632

Table truncated, full table size 8048 Kbytes.




Supplementary data files not provided
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