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Sample GSM84724 Query DataSets for GSM84724
Status Public on Nov 23, 2005
Title FL4 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 (FL4)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL4)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18880.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
1 105 92 98 82 7 10 106 91 102 85 8 9 0 0 27 32 27 28 22 31 5 7 17 17 .7 1.429 1.125 1.25 .937 3.904 80 415 1.706 .12 100 1280 9130 56 66 39 49 -50 91 81 10 1.414 90 9 .707 1.114 .5 .156
2 98 79 95 75 3 4 96 78 99 78 1 3 0 0 29 28 28 27 20 17 6 6 7 4 .75 1.333 3 .87 .947 2.89 80 327 6.604 .04 100 1440 9130 56 66 55 65 -50 78 74 4 1.32 77 3 .757 2.97 .401 1.571
3 776 945 99 74 677 871 532 596 102 77 433 522 0 0 592 806 28 27 94 96 92 93 1548 955 .777 1.287 1.206 1.26 1.277 2.254 208 851 1.361 .93 160 1600 9160 56 72 68 84 0 936 73 862 1.274 590 517 .785 1.194 .349 .255
4 2841 1231 106 71 2735 1160 3095 1379 109 76 2989 1308 0 0 986 474 42 34 100 100 100 96 3895 4297 2.358 .424 .438 .394 .418 2.292 80 316 .411 .92 100 1750 9140 57 67 86 96 0 1219 70 1149 .42 1365 1295 2.381 .433 -1.252 -1.207
5 489 287 105 72 384 215 552 294 123 82 447 222 0 0 251 147 79 50 78 71 75 68 599 669 1.786 .56 .497 .561 .605 2.128 32 190 .498 .79 70 1890 9160 60 67 101 108 0 284 71 213 .554 291 220 1.804 .492 -.851 -1.024
6 12551 2807 98 69 12453 2738 13784 3153 106 76 13686 3084 0 0 4257 991 44 34 100 100 100 100 15191 16770 4.548 .22 .225 .234 .222 2.1 80 419 .21 .93 100 2070 9140 57 67 118 128 0 2779 68 2711 .218 3122 3053 4.594 .223 -2.2 -2.164
7 911 359 92 68 819 291 926 357 94 71 834 289 0 0 422 168 26 25 94 92 94 82 1110 1123 2.814 .355 .347 .308 .373 1.904 52 313 .346 .92 90 2220 9130 56 65 133 142 0 355 67 288 .352 353 286 2.843 .343 -1.507 -1.543
8 85 66 90 68 -5 -2 82 63 91 70 -8 -5 0 0 21 21 23 26 11 11 0 1 -7 -13 null null null .744 .757 2.601 80 395 3.817 .15 100 2380 9130 56 66 149 159 -50 65 67 -2 null 62 null null null null null
9 235 336 84 66 151 270 235 345 86 68 151 279 0 0 81 110 22 24 93 98 88 95 421 430 .559 1.788 1.848 1.778 1.735 2.082 80 360 1.851 .8 100 2540 9140 57 67 165 175 0 333 65 267 1.77 342 276 .565 1.829 .824 .871
10 92 78 89 70 3 8 89 72 91 72 0 2 0 0 25 26 23 24 13 22 7 7 11 2 .375 2.667 null 1.079 1.32 4.642 80 380 4.394 .03 100 2690 9130 56 66 180 190 -50 77 69 8 2.64 71 2 .379 null 1.401 null
11 328 217 90 67 238 150 339 218 92 72 249 151 0 0 114 82 23 27 93 92 92 86 388 400 1.587 .63 .606 .579 .611 1.806 80 356 .624 .84 100 2860 9130 56 66 197 207 0 215 66 149 .624 216 150 1.603 .6 -.68 -.736
12 96 65 90 65 6 0 97 59 92 68 7 -6 0 0 27 23 21 29 27 11 10 1 6 1 null null null .805 .667 3.385 80 359 4.098 .1 100 3000 9130 56 66 211 221 -50 64 64 0 null 58 null null null null null
13 344 207 90 67 254 140 369 206 91 70 279 139 0 0 133 83 24 23 88 88 88 86 394 418 1.814 .551 .498 .547 .548 2.033 52 311 .531 .77 90 3170 9140 57 66 228 237 0 205 66 139 .546 204 138 1.832 .493 -.874 -1.02
14 87 64 89 64 -2 0 83 59 92 70 -6 -5 0 0 24 26 26 56 12 2 1 0 -2 -11 null null null 1.383 1.429 2.956 80 384 .975 .19 100 3320 9130 56 66 243 253 -50 63 63 0 null 58 null null null null null
15 308 244 86 64 222 180 324 258 88 69 238 194 0 0 116 99 24 56 92 85 88 77 402 432 1.233 .811 .815 .801 .797 2.283 80 380 .8 .82 100 3490 9130 56 66 260 270 0 242 63 178 .803 255 192 1.246 .807 -.317 -.309
16 629 667 85 63 544 604 568 536 86 65 483 473 0 0 393 457 22 22 88 97 87 94 1148 956 .901 1.11 .979 1.133 1.106 2.561 120 455 1.146 .89 120 3660 9130 55 67 276 288 0 660 62 598 1.099 531 468 .91 .97 .137 -.045
17 92 62 88 65 4 -3 90 61 90 66 2 -4 0 0 24 20 24 23 20 13 6 0 1 -2 null null null .982 1.163 3.732 80 337 .394 .09 100 3790 9130 56 66 290 300 -50 61 64 -3 null 60 null null null null null
18 388 234 96 72 292 162 426 235 104 75 330 163 0 0 125 85 35 30 90 93 90 90 454 493 1.802 .555 .494 .541 .573 1.486 32 207 .504 .82 70 3940 9120 56 63 306 313 0 232 71 160 .549 233 161 1.82 .489 -.864 -1.032
19 89 65 92 64 -3 1 88 63 96 66 -4 -1 0 0 23 21 29 24 10 12 0 1 -2 -5 null null null 1.097 1.125 3.847 80 424 .281 .09 100 4100 9120 55 65 321 331 -50 64 63 1 null 62 null null null null null
20 383 209 92 67 291 142 389 203 96 71 297 136 0 0 187 93 26 25 92 90 90 83 433 433 2.049 .488 .458 .485 .484 2.061 80 379 .434 .81 100 4270 9120 55 65 338 348 0 207 66 141 .483 201 135 2.07 .453 -1.049 -1.141

Total number of rows: 37632

Table truncated, full table size 7968 Kbytes.




Supplementary data files not provided
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