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Sample GSM84733 Query DataSets for GSM84733
Status Public on Nov 23, 2005
Title FL23 CR 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 (FL23)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL23)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24635.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
1 178 187 120 103 58 84 142 134 126 106 22 31 0 0 125 168 32 36 34 46 18 31 142 53 .69 1.448 1.409 1.582 1.184 3.236 32 195 1.55 .65 70 1940 8570 69 76 46 53 0 220 121 99 1.704 158 36 .587 1.658 .769 .729
2 137 130 123 105 14 25 132 122 126 111 9 17 0 0 43 52 28 38 25 32 12 10 39 26 .56 1.786 1.889 1.549 1.546 3.734 80 386 .797 .34 100 2070 8560 67 77 58 68 -50 153 124 29 2.101 144 20 .476 2.222 1.071 1.152
3 844 713 132 116 712 597 879 702 136 116 747 586 0 0 257 169 33 36 100 100 98 100 1309 1333 1.193 .838 .784 .902 .817 1.657 80 375 .79 .92 100 2240 8570 68 78 75 85 0 839 136 702 .986 826 689 1.014 .923 -.02 -.116
4 1936 724 132 119 1804 605 2113 746 136 123 1981 627 0 0 701 203 33 37 98 100 97 98 2409 2608 2.982 .335 .317 .381 .335 1.892 80 358 .304 .92 100 2400 8570 68 78 91 101 0 852 140 712 .395 878 738 2.535 .372 -1.342 -1.425
5 419 320 129 119 290 201 430 313 130 123 301 194 0 0 106 99 28 37 100 98 98 93 491 495 1.443 .693 .645 .678 .68 1.936 80 344 .663 .72 100 2550 8570 68 78 106 116 0 376 140 236 .815 368 228 1.226 .758 -.294 -.399
6 10853 2865 128 111 10725 2754 11710 3000 128 117 11582 2889 0 0 3777 830 30 35 100 100 100 100 13479 14471 3.894 .257 .249 .271 .262 1.532 80 343 .236 .94 100 2700 8570 68 78 121 131 0 3371 131 3240 .302 3529 3399 3.31 .293 -1.727 -1.769
7 393 248 126 112 267 136 402 225 126 120 276 113 0 0 192 101 29 37 85 90 82 77 403 389 1.963 .509 .409 .513 .49 2.35 80 363 .409 .67 100 2850 8560 67 77 136 146 -100 292 132 160 .599 265 133 1.669 .482 -.739 -1.054
8 135 132 122 113 13 19 137 130 125 117 15 17 0 0 32 44 28 36 31 33 10 11 32 32 .684 1.462 1.133 .978 1.131 4.891 80 394 5.934 .11 100 3010 8560 67 77 152 162 -50 155 133 22 1.719 153 20 .582 1.333 .782 .415
9 231 165 112 109 119 56 238 162 116 110 126 53 0 0 69 56 27 33 88 58 82 40 175 179 2.125 .471 .421 .47 .512 3.14 80 370 .539 .46 100 3180 8570 68 78 169 179 0 194 128 66 .554 191 62 1.806 .495 -.853 -1.015
10 122 129 116 107 6 22 116 114 117 110 0 7 0 0 37 83 28 36 20 28 6 13 28 7 .273 3.667 null 1.589 1.388 3.435 80 379 4.347 .26 100 3330 8560 67 77 184 194 -50 152 126 26 4.314 134 8 .232 null 2.109 null
11 339 212 132 120 207 92 349 199 136 122 217 79 0 0 113 76 33 38 90 73 88 53 299 296 2.25 .444 .364 .402 .451 2.102 52 314 .411 .65 90 3490 8550 66 75 200 209 0 249 141 108 .523 234 93 1.913 .428 -.935 -1.223
12 197 247 152 131 45 116 171 154 155 134 19 23 0 0 125 269 35 42 32 35 15 18 161 42 .388 2.578 1.211 1.303 1.37 3.526 80 398 2.898 .63 100 3640 8550 66 76 215 225 -50 291 154 136 3.033 181 27 .33 1.424 1.601 .51
13 371 206 153 137 218 69 373 207 155 139 220 70 0 0 110 61 34 40 92 71 90 36 287 290 3.159 .317 .318 .319 .283 1.962 52 324 .321 .6 90 3800 8560 67 76 231 240 0 242 161 81 .372 244 82 2.686 .374 -1.425 -1.418
14 207 255 148 133 59 122 165 158 151 135 17 25 0 0 123 271 34 37 31 38 18 22 181 42 .484 2.068 1.471 1.764 1.455 4.409 80 406 2.686 .69 100 3960 8550 66 76 247 257 -50 300 156 144 2.433 186 29 .411 1.73 1.283 .791
15 394 234 148 127 246 107 425 234 149 128 277 107 0 0 107 74 34 37 92 82 92 69 353 384 2.299 .435 .386 .385 .426 2.174 52 313 .459 .69 90 4120 8560 67 76 263 272 0 275 149 126 .512 275 126 1.954 .454 -.967 -1.138
16 218 260 156 132 62 128 165 172 177 154 9 40 0 0 157 317 116 104 15 23 8 17 190 49 .484 2.065 4.444 1.671 1.452 2.995 80 394 1.987 .73 100 4270 8550 66 76 278 288 -100 306 155 151 2.429 202 47 .412 5.229 1.28 2.386
17 169 151 150 131 19 20 154 139 173 153 4 8 0 0 63 61 123 108 6 7 2 2 39 12 .95 1.053 2 1.418 1.292 3.535 80 357 .805 .79 100 4430 8550 66 76 294 304 -50 178 154 24 1.238 164 9 .808 2.353 .308 1.234
18 371 239 134 118 237 121 390 234 134 121 256 116 0 0 166 74 29 36 84 89 80 73 358 372 1.959 .511 .453 .567 .457 3.63 120 471 .343 .47 120 4580 8560 66 78 308 320 0 281 139 142 .601 275 136 1.665 .533 -.735 -.908
19 135 124 133 117 2 7 126 121 135 120 -7 4 0 0 44 46 27 38 20 20 11 7 9 -3 .286 3.5 null 1.106 .867 3.629 80 372 4.043 .08 100 4740 8550 66 76 325 335 -50 146 138 8 4.118 142 5 .243 null 2.042 null
20 313 263 133 120 180 143 213 195 134 123 80 75 0 0 545 230 29 37 65 68 55 50 323 155 1.259 .794 .938 .905 .909 3.412 80 378 .194 .34 100 4900 8550 66 76 341 351 -100 309 141 168 .935 229 88 1.07 1.103 -.098 .141

Total number of rows: 37632

Table truncated, full table size 8094 Kbytes.




Supplementary data files not provided
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