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Sample GSM84744 Query DataSets for GSM84744
Status Public on Nov 23, 2005
Title FL7 PR 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 (FL7)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL7)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18729.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 84 78 85 75 -1 3 80 77 86 77 -5 2 0 0 22 20 24 23 15 16 1 2 2 -3 null null null .958 .969 3.283 80 414 .377 .04 100 1230 9060 89 99 42 52 -50 70 68 3 null 69 2 null null null null
2 84 72 86 75 -2 -3 79 69 111 110 -7 -6 0 0 22 22 73 94 0 0 0 0 -5 -13 null null null 1.047 1.071 2.596 80 366 1.632 .8 100 1380 9060 89 99 57 67 -50 65 68 -3 null 62 null null null null null
3 845 959 93 74 752 885 893 992 118 115 800 918 0 0 342 452 78 101 91 93 91 92 1637 1718 .85 1.177 1.148 1.185 1.23 2.208 80 385 1.257 .85 110 1540 9070 89 100 72 83 0 864 67 797 1.06 894 827 .943 1.034 .084 .048
4 1628 760 87 69 1541 691 1769 825 88 72 1682 756 0 0 591 231 25 31 98 100 98 100 2232 2438 2.23 .448 .449 .49 .434 2.052 80 378 .41 .91 110 1690 9070 89 100 87 98 0 685 62 623 .404 743 681 2.475 .405 -1.308 -1.304
5 434 345 86 71 348 274 441 366 87 73 355 295 0 0 144 126 23 22 96 97 96 93 622 650 1.27 .787 .831 .749 .761 2.123 80 351 .792 .85 100 1850 9060 89 99 104 114 0 311 64 247 .709 330 266 1.41 .749 -.495 -.418
6 8612 2753 83 75 8529 2678 9586 3019 86 77 9503 2944 0 0 3223 1179 23 21 100 100 100 97 11207 12447 3.185 .314 .31 .29 .308 2.186 80 413 .297 .88 110 2000 9060 88 99 118 129 0 2480 68 2413 .283 2720 2652 3.535 .279 -1.822 -1.841
7 635 370 81 74 554 296 604 373 83 76 523 299 0 0 300 158 22 21 96 96 96 93 850 822 1.872 .534 .572 .476 .524 2.007 80 344 .5 .88 100 2170 9060 89 99 136 146 0 333 67 267 .481 336 269 2.078 .515 -1.055 -.957
8 88 80 82 72 6 8 83 75 82 74 1 3 0 0 25 31 20 21 25 25 10 11 14 4 .75 1.333 3 .838 .801 3.932 80 343 -1 -1 100 2310 9060 89 99 150 160 -50 72 65 7 1.201 68 3 .833 2.703 .264 1.434
9 244 438 82 72 162 366 265 483 85 75 183 411 0 0 97 142 24 20 86 96 81 96 528 594 .443 2.259 2.246 2.2 1.996 2.113 80 349 2.267 .8 100 2480 9070 90 100 167 177 0 395 65 330 2.035 435 370 .491 2.023 1.025 1.017
10 86 82 83 72 3 10 80 77 86 74 -3 5 0 0 24 24 23 20 20 30 5 10 13 2 .3 3.333 null .925 .833 3.472 80 363 3.54 .05 100 2630 9060 89 99 182 192 -50 74 65 9 3.003 69 5 .333 null 1.586 null
11 248 229 83 71 165 158 254 244 86 73 171 173 0 0 89 79 23 18 90 93 86 88 323 344 1.044 .958 1.012 .98 .945 2.045 80 366 .905 .79 100 2800 9060 89 99 199 209 0 206 64 142 .863 220 156 1.159 .911 -.213 -.134
12 95 76 88 71 7 5 92 74 91 75 4 3 0 0 22 23 24 21 17 16 5 7 12 7 1.4 .714 .75 .758 .704 3.213 80 359 .583 .12 100 2940 9050 88 98 213 223 -50 68 64 5 .644 67 3 1.554 .676 -.636 -.566
13 317 329 89 70 228 259 326 366 92 73 237 296 0 0 126 146 24 20 92 92 91 88 487 533 .88 1.136 1.249 1.056 1.179 2.284 80 351 1.179 .84 100 3100 9060 89 99 229 239 0 296 63 233 1.023 330 267 .977 1.125 .033 .17
14 97 98 87 70 10 28 89 81 90 76 2 11 0 0 45 64 27 54 18 15 7 7 38 13 .357 2.8 5.5 1.172 1.095 4.575 80 367 3.257 .2 100 3250 9050 88 98 244 254 -50 88 63 25 2.523 73 10 .396 4.955 1.335 2.309
15 308 324 85 68 223 256 332 352 88 72 247 284 0 0 114 109 23 20 91 95 88 93 479 531 .871 1.148 1.15 1.246 1.172 2.495 80 380 1.095 .81 100 3420 9060 89 99 261 271 0 292 61 231 1.034 317 256 .967 1.036 .049 .051
16 578 849 88 71 490 778 504 759 90 74 416 688 0 0 372 576 24 21 92 92 90 91 1268 1104 .63 1.588 1.654 1.395 1.543 2.864 120 412 1.635 .91 120 3590 9080 90 102 277 289 0 765 64 701 1.43 684 620 .699 1.49 .516 .575
17 92 70 82 70 10 0 92 69 86 73 10 -1 0 0 26 21 23 21 30 15 8 1 10 9 null null null 1.026 .87 3.761 80 313 -1 -1 100 3720 9050 88 98 291 301 -50 63 63 0 null 62 null null null null null
18 376 637 87 76 289 561 406 655 92 79 319 579 0 0 137 271 27 24 93 95 93 93 850 898 .515 1.941 1.815 1.831 1.831 2.071 80 356 2.193 .83 100 3870 9060 89 99 306 316 0 574 68 505 1.749 590 522 .572 1.635 .806 .709
19 90 80 90 75 0 5 88 80 93 78 -2 5 0 0 26 24 25 23 18 16 2 5 5 3 null null null .702 .56 4.224 80 379 -1 -1 100 4030 9050 88 98 322 332 -50 72 68 5 null 72 5 null null null null
20 332 339 88 72 244 267 338 334 95 78 250 262 0 0 120 156 102 75 87 86 65 77 511 512 .914 1.094 1.048 .969 1.026 2.045 80 365 .969 .87 100 4190 9050 88 98 338 348 0 305 65 241 .986 301 236 1.014 .944 -.021 -.083

Total number of rows: 37632

Table truncated, full table size 8164 Kbytes.




Supplementary data files not provided
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