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Sample GSM84714 Query DataSets for GSM84714
Status Public on Nov 23, 2005
Title FL11b CR
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 lymph node (FL11)
Organism Homo sapiens
Characteristics Follicular lymphoma lymph node (FL11)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14683.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 GPL3042
Series (2)
GSE3646 Follicular lymphoma and normal lymphoid tissue comparisons
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
1 483 745 139 143 344 602 398 625 173 191 259 482 0 0 333 541 111 152 64 70 54 58 946 741 .571 1.75 1.861 1.803 1.772 2.034 120 544 1.695 .93 120 1790 7740 60 72 57 69 -100 1064 204 860 2.5 893 689 .4 2.659 1.322 1.411
2 448 426 123 134 325 292 373 349 149 163 250 215 0 0 294 252 70 104 71 68 59 59 617 465 1.113 .898 .86 .893 .939 3.54 32 161 1.072 .82 70 1940 7750 63 70 74 81 -100 609 191 417 1.284 499 307 .779 1.229 .36 .297
3 2671 1276 132 128 2539 1148 2447 1331 146 162 2315 1203 0 0 1587 632 72 188 100 92 96 88 3687 3518 2.212 .452 .52 .481 .453 1.568 52 280 .415 .88 90 2070 7720 59 68 86 95 0 1823 183 1640 .646 1901 1719 1.548 .742 -.631 -.43
4 217 194 128 125 89 69 133 121 147 171 5 -4 0 0 214 198 79 184 22 15 16 11 158 1 1.29 .775 null 1.59 1.412 3.457 80 396 2.415 .52 100 2190 7720 59 69 98 108 -50 277 179 99 1.108 173 null .903 null .147 null
5 1101 651 138 151 963 500 995 618 188 246 857 467 0 0 635 319 119 217 94 76 88 55 1463 1324 1.926 .519 .545 .546 .493 1.893 52 214 .521 .8 80 2360 7730 61 69 116 124 0 930 216 714 .742 883 667 1.348 .778 -.431 -.361
6 235 267 126 130 109 137 141 161 150 175 15 31 0 0 209 220 82 153 33 26 26 21 246 46 .796 1.257 2.067 1.513 1.387 3.19 80 332 1.253 .82 100 2470 7720 59 69 126 136 -100 381 186 196 1.796 230 44 .557 2.952 .844 1.562
7 1116 588 117 120 999 468 918 502 119 124 801 382 0 0 556 349 21 33 100 100 100 100 1467 1183 2.135 .468 .477 .419 .409 1.404 32 216 .513 .95 70 2620 7720 60 67 142 149 0 840 171 669 .669 717 546 1.494 .681 -.579 -.554
8 618 312 116 124 502 188 585 330 120 134 469 206 0 0 215 141 26 55 100 81 100 62 690 675 2.67 .375 .439 .328 .357 2.083 32 202 .372 .75 70 2760 7720 60 67 156 163 0 446 177 269 .535 471 294 1.869 .627 -.902 -.672
9 458 306 119 131 339 175 302 222 129 145 183 91 0 0 427 202 50 72 84 56 75 43 514 274 1.937 .516 .497 .615 .614 3.437 32 166 .497 .81 60 2890 7730 62 68 170 176 -100 437 187 250 .737 317 130 1.356 .71 -.439 -.493
10 395 346 123 124 272 222 380 355 132 136 257 231 0 0 107 100 41 47 100 91 100 83 494 488 1.225 .816 .899 .774 .777 1.381 12 104 .805 .85 50 3020 7720 61 66 183 188 -100 494 177 317 1.166 507 330 .858 1.284 .222 .361
11 1027 610 142 164 885 446 623 471 235 353 481 307 0 0 1115 514 215 470 63 34 51 15 1331 788 1.984 .504 .638 .653 .612 2.212 52 270 .465 .86 90 3170 7710 58 67 196 205 -100 871 234 637 .72 673 439 1.389 .912 -.474 -.133
12 520 380 136 140 384 240 259 251 173 227 123 111 0 0 526 314 122 222 50 31 40 21 624 234 1.6 .625 .902 .785 .744 2.671 32 125 .665 .87 60 3290 7730 62 68 210 216 -100 543 200 343 .893 359 159 1.12 1.289 -.163 .366
13 523 521 125 120 398 401 502 509 130 123 377 389 0 0 214 161 34 35 100 100 93 100 799 766 .993 1.008 1.032 1.119 1.011 1.52 32 197 .95 .94 70 3450 7730 61 68 225 232 -100 744 171 573 1.439 727 556 .695 1.474 .525 .56
14 1399 683 128 132 1271 551 1399 680 152 169 1271 548 0 0 519 229 102 159 100 100 100 90 1822 1819 2.307 .434 .431 .433 .422 1.408 32 124 .422 .91 60 3580 7730 62 68 239 245 0 976 189 787 .619 971 783 1.615 .616 -.691 -.699
15 279 235 137 136 142 99 133 145 179 213 -4 9 0 0 350 246 140 241 18 15 17 10 241 5 1.434 .697 null .97 .955 2.383 80 342 .833 .83 100 3690 7720 59 69 248 258 -50 336 194 141 .996 207 13 1.004 null -.006 null
16 2353 1694 130 125 2223 1569 2531 1825 136 146 2401 1700 0 0 613 505 40 107 100 100 100 96 3792 4101 1.417 .706 .708 .678 .691 1.291 32 215 .724 .97 70 3840 7720 60 67 264 271 0 2420 179 2241 1.008 2607 2429 .992 1.011 .012 .016
17 688 651 139 134 549 517 592 605 185 196 453 471 0 0 456 399 138 211 78 69 63 51 1066 924 1.062 .942 1.04 .923 .943 1.824 52 244 1.032 .88 90 3990 7730 60 69 278 287 -100 930 191 739 1.345 864 673 .743 1.485 .428 .571
18 826 419 133 128 693 291 831 393 146 140 698 265 0 0 241 137 57 71 100 100 100 90 984 963 2.381 .42 .38 .411 .395 1.474 32 175 .418 .86 70 4110 7720 60 67 291 298 0 599 183 416 .6 561 379 1.667 .542 -.737 -.883
19 536 315 128 119 408 196 575 324 133 122 447 205 0 0 164 80 27 32 100 100 100 93 604 652 2.082 .48 .459 .47 .462 1.448 32 222 .462 .87 70 4250 7720 60 67 305 312 0 450 170 280 .686 463 293 1.457 .655 -.543 -.61
20 1269 1212 129 127 1140 1085 1302 1305 132 127 1173 1178 0 0 707 594 25 30 100 100 100 100 2225 2351 1.051 .952 1.004 1.07 .993 1.489 32 206 .908 .97 70 4380 7730 61 68 318 325 0 1731 181 1550 1.36 1864 1683 .735 1.435 .443 .521

Total number of rows: 39168

Table truncated, full table size 8572 Kbytes.




Supplementary data files not provided
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