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Sample GSM84727 Query DataSets for GSM84727
Status Public on Nov 23, 2005
Title FL12 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 (FL12)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL12)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18874.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) [email protected]
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
1 144 134 134 121 10 13 143 128 141 134 9 7 0 0 29 49 43 68 12 12 2 2 23 16 .769 1.3 .778 1.867 2.067 3.42 80 423 7.768 .21 100 1440 8630 86 96 47 57 -50 174 157 17 1.688 166 9 .592 1.01 .756 .014
2 127 112 123 118 4 -6 126 108 128 128 3 -10 0 0 27 34 36 63 10 2 1 0 -2 -7 null null null 1.386 1.107 4.096 80 372 2.841 .23 100 1600 8630 86 96 63 73 -50 145 153 -8 null 140 null null null null null
3 1414 1188 124 121 1290 1067 1582 1202 151 137 1458 1081 0 0 805 670 93 91 95 96 88 90 2357 2539 1.209 .827 .741 .825 .804 1.856 80 418 .882 .91 110 1750 8630 85 96 77 88 0 1543 157 1386 1.074 1561 1404 .931 .963 .103 -.055
4 3468 1167 127 121 3341 1046 3856 1210 149 135 3729 1089 0 0 1319 411 85 92 96 100 96 95 4387 4818 3.194 .313 .292 .341 .293 1.888 80 370 .298 .93 100 1910 8640 87 97 94 104 0 1516 157 1358 .407 1571 1414 2.459 .379 -1.298 -1.399
5 681 312 124 114 557 198 714 303 126 116 590 189 0 0 353 131 31 39 90 90 87 82 755 779 2.813 .355 .32 .354 .368 2.275 80 402 .321 .82 100 2080 8640 87 97 111 121 0 405 148 257 .462 394 245 2.166 .416 -1.115 -1.265
6 18908 2590 123 116 18785 2474 20978 2632 128 123 20855 2516 0 0 7539 950 38 53 100 100 100 100 21259 23371 7.593 .132 .121 .161 .126 2.464 80 374 .115 .9 100 2240 8640 87 97 127 137 0 3364 151 3213 .171 3418 3268 5.847 .157 -2.548 -2.674
7 1199 293 124 118 1075 175 1334 280 131 123 1210 162 0 0 531 126 39 55 96 76 96 63 1250 1372 6.143 .163 .134 .163 .167 2.347 52 301 .161 .77 90 2390 8630 86 95 142 151 0 381 153 227 .211 364 210 4.73 .174 -2.242 -2.524
8 128 127 119 120 9 7 124 112 122 125 5 -8 0 0 35 80 32 43 23 15 6 6 16 -3 1.286 .778 null 1.345 1.385 4.77 80 401 -1 -1 100 2540 8630 86 96 157 167 -50 165 156 9 1.01 145 null .99 null .014 null
9 424 237 124 127 300 110 443 235 126 130 319 108 0 0 161 73 32 45 90 80 90 61 410 427 2.727 .367 .339 .332 .375 2.036 52 312 .373 .68 90 2700 8630 86 95 173 182 0 308 165 143 .476 305 140 2.1 .44 -1.07 -1.185
10 128 121 124 122 4 -1 127 119 126 131 3 -3 0 0 30 46 34 76 12 6 3 1 3 0 null null null 1.379 1.528 4.206 80 386 26.456 .03 100 2850 8630 86 96 188 198 -50 157 158 -1 null 155 null null null null null
11 457 212 116 120 341 92 457 209 122 128 341 89 0 0 180 71 36 55 90 63 90 42 433 430 3.707 .27 .261 .249 .278 3.242 80 371 .233 .5 100 3010 8630 86 96 204 214 0 275 156 119 .35 271 116 2.854 .339 -1.513 -1.561
12 126 111 114 120 12 -9 122 111 117 124 8 -9 0 0 39 40 32 46 21 10 3 0 3 -1 null null null 1.647 1.9 4.416 80 379 27.133 .05 100 3160 8620 85 95 219 229 -50 144 156 -12 null 144 null null null null null
13 526 264 117 118 409 146 557 252 119 122 440 134 0 0 218 94 32 40 90 84 88 75 555 574 2.801 .357 .305 .338 .326 2.102 52 313 .319 .72 90 3320 8630 86 95 235 244 0 343 153 190 .464 327 174 2.157 .396 -1.109 -1.338
14 132 124 116 115 16 9 127 122 121 123 11 7 0 0 37 54 32 51 18 15 6 2 25 18 1.778 .563 .636 1.663 1.923 4.479 80 408 .109 .06 100 3470 8620 85 95 250 260 -50 161 149 12 .731 158 9 1.369 .826 -.453 -.275
15 538 292 118 112 420 180 555 295 121 120 437 183 0 0 219 107 32 51 91 88 90 75 600 620 2.333 .429 .419 .443 .413 2.407 80 400 .396 .8 100 3640 8630 86 96 267 277 0 379 145 234 .557 383 238 1.797 .544 -.845 -.879
16 1217 772 119 111 1098 661 1147 633 122 118 1028 522 0 0 877 572 29 41 95 98 93 90 1759 1550 1.661 .602 .508 .578 .566 2.391 80 413 .596 .89 110 3810 8630 85 96 283 294 0 1003 144 858 .782 822 678 1.279 .659 -.355 -.601
17 128 126 119 113 9 13 131 118 126 124 12 5 0 0 33 75 35 87 17 3 2 2 22 17 .692 1.444 .417 1.702 2.333 3.78 80 357 12.073 .13 100 3940 8620 85 95 297 307 -50 164 147 17 1.876 153 6 .533 .541 .908 -.886
18 501 293 125 114 376 179 513 268 132 125 388 154 0 0 179 139 41 86 95 73 90 45 555 542 2.101 .476 .397 .442 .445 2.086 80 375 .612 .61 100 4100 8630 86 96 313 323 0 381 148 232 .618 348 200 1.617 .515 -.694 -.956
19 127 124 124 120 3 4 126 119 128 124 2 -1 0 0 33 39 36 43 13 17 3 1 7 1 .75 1.333 null 1.115 1.205 3.989 80 405 4.308 .09 100 4250 8620 85 95 328 338 -50 161 156 5 1.732 155 null .577 null .792 null
20 504 239 118 117 386 122 515 235 122 122 397 118 0 0 202 74 31 48 94 90 92 57 508 515 3.164 .316 .297 .353 .33 2.492 52 326 .314 .7 90 4420 8620 85 94 345 354 0 310 152 158 .41 305 153 2.436 .386 -1.285 -1.373

Total number of rows: 37632

Table truncated, full table size 8218 Kbytes.




Supplementary data files not provided
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