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Sample GSM84726 Query DataSets for GSM84726
Status Public on Nov 23, 2005
Title FL6 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 (FL6)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL6)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18873.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 56 52 53 54 3 -2 54 45 57 56 1 -9 0 0 16 24 16 22 20 17 5 5 1 -8 null null null 1.469 1.625 3.068 80 424 -1 -1 100 1450 9280 63 73 32 42 -50 88 92 -3 null 76 null null null null null
2 57 59 54 58 3 1 53 54 56 59 -1 -4 0 0 16 22 16 24 16 13 5 5 4 -5 3 .333 null 1.15 1.244 3.332 80 403 -1 -1 100 1610 9280 63 73 48 58 -50 100 98 2 .565 92 null 1.77 null -.824 null
3 415 270 56 54 359 216 396 191 70 58 340 137 0 0 317 221 95 25 68 75 56 65 575 477 1.662 .602 .403 .677 .754 3.814 32 171 .454 .49 60 1770 9290 66 72 66 72 0 458 92 366 1.02 324 232 .981 .683 .028 -.55
4 1390 423 59 56 1331 367 1504 408 62 60 1445 352 0 0 423 201 18 25 100 95 100 95 1698 1797 3.627 .276 .244 .257 .292 2.016 80 389 .275 .85 100 1930 9280 63 73 80 90 0 717 95 622 .467 692 597 2.14 .413 -1.097 -1.276
5 413 229 58 59 355 170 432 201 60 62 374 142 0 0 137 98 18 39 100 98 98 86 525 516 2.088 .479 .38 .462 .455 2.05 80 373 .46 .77 100 2080 9280 63 73 95 105 0 388 100 288 .812 341 241 1.232 .644 -.301 -.636
6 7771 1201 58 57 7713 1144 8226 1175 59 61 8168 1118 0 0 2373 436 18 37 100 100 100 100 8857 9286 6.742 .148 .137 .15 .144 1.742 80 374 .138 .9 100 2240 9280 63 73 111 121 0 2036 97 1939 .251 1992 1895 3.978 .232 -1.992 -2.108
7 471 140 59 56 412 84 466 144 61 60 407 88 0 0 198 48 17 23 100 84 100 76 496 495 4.905 .204 .216 .206 .183 2.388 52 293 .207 .66 90 2390 9270 62 71 126 135 0 237 95 142 .346 244 149 2.894 .366 -1.533 -1.448
8 58 52 55 55 3 -3 56 51 57 60 1 -4 0 0 16 20 17 38 18 3 2 0 0 -3 null null null .999 1 4 80 392 .073 .07 100 2540 9270 62 72 141 151 -50 88 93 -5 null 86 null null null null null
9 140 106 57 58 83 48 139 104 57 60 82 46 0 0 49 31 15 25 90 75 86 41 131 128 1.729 .578 .561 .633 .583 3.387 80 373 .499 .5 100 2710 9280 63 73 158 168 0 180 98 81 .98 176 78 1.02 .951 -.029 -.073
10 65 65 58 57 7 8 62 62 59 63 4 5 0 0 17 29 15 33 31 16 11 3 15 9 .875 1.143 1.25 1.246 1.646 3.55 80 380 28.658 .05 100 2860 9270 62 72 173 183 -50 110 97 14 1.937 105 8 .516 2.119 .954 1.083
11 983 625 56 57 927 568 213 113 58 61 157 56 0 0 2076 1202 15 32 97 68 93 45 1495 213 1.632 .613 .357 .409 .422 3.082 80 346 .555 .91 100 3030 9280 63 73 190 200 -100 1059 97 963 1.039 192 95 .963 .605 .055 -.726
12 56 57 55 57 1 0 54 57 58 58 -1 0 0 0 15 21 16 22 18 16 1 3 1 -1 null null null 1.344 1.291 4.288 80 351 11.914 .04 100 3170 9270 62 72 204 214 -50 97 97 0 null 97 0 null null null null
13 261 108 59 57 202 51 263 101 62 60 204 44 0 0 90 53 18 24 98 61 98 46 253 248 3.961 .252 .216 .23 .266 2.629 80 367 .256 .58 100 3340 9270 62 72 221 231 0 183 97 86 .428 171 75 2.337 .366 -1.225 -1.452
14 65 66 59 57 6 9 63 62 61 60 4 5 0 0 17 27 17 24 28 27 3 10 15 9 .667 1.5 1.25 1.29 1.314 4.912 80 365 .03 .03 100 3480 9260 61 71 235 245 -50 112 97 15 2.542 105 8 .393 2.119 1.346 1.083
15 298 169 61 56 237 113 307 173 63 59 246 117 0 0 105 70 17 24 95 88 95 77 350 363 2.097 .477 .476 .449 .484 2.595 80 432 .462 .78 100 3650 9270 62 72 252 262 0 286 95 192 .808 293 198 1.237 .806 -.307 -.311
16 567 421 64 55 503 366 386 368 67 58 322 313 0 0 454 318 18 23 90 80 80 76 869 635 1.374 .728 .972 .899 .717 3.13 52 236 .676 .85 80 3840 9290 65 73 272 280 -100 714 93 620 1.233 624 531 .811 1.648 .302 .72
17 65 65 63 57 2 8 61 63 65 60 -2 6 0 0 17 28 18 24 16 27 3 8 10 4 .25 4 null 1.317 1.499 4.192 80 331 11.132 .07 100 3950 9260 61 71 282 292 -50 110 97 14 6.78 107 10 .148 null 2.761 null
18 258 150 60 57 198 93 263 143 63 60 203 86 0 0 88 61 18 22 98 86 97 75 291 289 2.129 .47 .424 .391 .482 2.334 80 378 .46 .74 100 4100 9260 61 71 297 307 0 254 97 158 .796 242 146 1.256 .718 -.329 -.478
19 63 62 60 57 3 5 60 58 63 59 0 1 0 0 17 22 17 23 23 23 5 3 8 1 .6 1.667 null 1.045 1.12 3.62 80 361 .11 .06 100 4260 9260 61 71 313 323 -50 105 97 8 2.825 98 2 .354 null 1.498 null
20 83 67 61 57 22 10 67 64 63 59 6 7 0 0 50 29 17 24 36 27 23 11 32 13 2.2 .455 1.167 1.115 .962 5.569 80 350 .318 .16 100 4410 9260 61 71 328 338 -50 114 97 17 .77 108 12 1.298 1.977 -.376 .984

Total number of rows: 37632

Table truncated, full table size 7907 Kbytes.




Supplementary data files not provided
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