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Sample GSM84725 Query DataSets for GSM84725
Status Public on Nov 23, 2005
Title FL9 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 (FL9)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL9)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18865.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 80 56 81 44 -1 12 75 49 82 46 -6 5 0 0 25 31 25 17 15 22 3 5 11 -1 null null null .641 .65 4.542 80 410 .349 .08 100 1280 9240 63 73 39 49 -50 72 56 15 null 63 6 null null null null
2 73 48 76 45 -3 3 74 50 79 49 -2 5 0 0 20 14 25 24 7 2 0 0 0 3 null null null .898 .867 3.2 80 377 .05 .04 100 1430 9230 62 72 54 64 -50 62 58 4 null 64 6 null null null null
3 1280 944 75 44 1205 900 1394 984 80 49 1319 940 0 0 438 369 27 29 100 100 100 98 2105 2259 1.339 .747 .713 .683 .76 2.017 80 428 .755 .91 110 1600 9230 61 72 70 81 0 1210 56 1154 .958 1262 1205 1.044 .914 -.063 -.13
4 2353 595 73 47 2280 548 2614 639 78 51 2541 592 0 0 777 198 27 20 100 100 100 97 2828 3133 4.161 .24 .233 .24 .237 2.171 80 403 .218 .86 110 1750 9240 62 73 85 96 0 763 60 703 .308 819 759 3.245 .299 -1.698 -1.743
5 543 281 76 44 467 237 574 274 78 46 498 230 0 0 226 103 24 16 93 97 93 96 704 728 1.97 .507 .462 .514 .476 2.749 80 355 .435 .82 100 1910 9250 64 74 102 112 0 360 56 304 .651 351 295 1.537 .592 -.62 -.756
6 13516 2853 76 47 13440 2806 15056 3163 78 48 14980 3116 0 0 4645 1046 22 15 100 100 100 100 16246 18096 4.79 .209 .208 .21 .205 2.041 80 372 .186 .86 100 2070 9240 63 73 118 128 0 3658 60 3597 .268 4055 3995 3.736 .267 -1.901 -1.907
7 760 216 75 43 685 173 824 244 76 47 749 201 0 0 267 85 22 37 100 86 98 78 858 950 3.96 .253 .268 .247 .255 2.15 52 293 .228 .8 90 2220 9230 62 71 133 142 0 277 55 222 .324 313 258 3.088 .344 -1.627 -1.539
8 69 43 73 41 -4 2 67 42 76 47 -6 1 0 0 21 15 26 65 7 1 2 0 -2 -5 null null null .869 .8 2.948 80 405 9.373 .26 100 2370 9230 62 72 148 158 -50 55 53 3 null 54 1 null null null null
9 247 227 71 46 176 181 260 237 73 48 189 191 0 0 93 78 20 15 90 95 88 93 357 380 .972 1.028 1.011 .988 .929 2.555 80 370 .958 .76 100 2540 9240 63 73 165 175 0 291 59 232 1.318 304 245 .758 1.296 .399 .374
10 84 45 71 44 13 1 85 43 74 45 14 -1 0 0 24 19 22 15 32 13 8 6 14 13 13 .077 null .702 .765 3.064 80 379 .124 .09 100 2690 9230 62 72 180 190 -50 58 56 1 .099 55 null 10.14 null -3.342 null
11 329 218 77 50 252 168 342 220 79 52 265 170 0 0 115 79 22 20 94 94 94 94 420 435 1.5 .667 .642 .649 .669 1.524 52 304 .641 .84 90 2850 9230 62 71 196 205 0 279 64 215 .855 282 218 1.17 .822 -.227 -.282
12 82 55 79 49 3 6 78 51 80 51 -1 2 0 0 31 29 22 18 18 18 11 11 9 1 .5 2 null .632 .529 4.181 80 380 .141 .03 100 3000 9230 62 72 211 221 -50 71 63 8 2.564 65 3 .39 null 1.358 null
13 332 210 74 42 258 168 358 213 79 44 284 171 0 0 128 80 37 14 93 93 90 93 426 455 1.536 .651 .602 .649 .668 2.149 80 379 .588 .84 100 3160 9230 62 72 227 237 0 269 54 215 .835 273 219 1.198 .772 -.26 -.373
14 71 50 71 46 0 4 70 50 76 48 -1 4 0 0 20 15 38 17 3 21 0 3 4 3 null null null 1.063 1 5.05 80 365 85.376 .03 100 3320 9230 62 72 243 253 -50 64 59 5 null 64 5 null null null null
15 370 237 87 48 283 189 379 258 101 64 292 210 0 0 126 103 55 48 91 87 88 81 472 502 1.497 .668 .719 .604 .656 2.399 80 370 .659 .81 100 3480 9230 62 72 259 269 0 304 62 242 .856 331 269 1.168 .922 -.224 -.117
16 547 686 87 51 460 635 263 266 99 61 176 215 0 0 529 760 49 39 72 83 66 73 1095 391 .724 1.38 1.222 1.221 1.159 3.223 120 569 1.482 .88 130 3660 9220 59 72 275 288 -100 879 65 814 1.77 341 276 .565 1.566 .824 .647
17 76 49 81 47 -5 2 70 46 91 52 -11 -1 0 0 22 20 41 21 5 12 0 3 -3 -12 null null null .602 .599 3.042 80 326 .237 .21 100 3790 9230 62 72 290 300 -50 63 60 3 null 59 null null null null null
18 367 199 78 45 289 154 374 206 82 48 296 161 0 0 115 77 28 18 98 91 96 87 443 457 1.877 .533 .544 .468 .534 2.146 80 353 .523 .87 100 3950 9210 60 70 306 316 0 255 58 197 .683 264 206 1.464 .697 -.55 -.52
19 82 50 78 46 4 4 78 48 82 50 0 2 0 0 25 18 25 18 21 17 3 6 8 2 1 1 null .589 .5 3.103 80 377 .045 .03 100 4100 9230 62 72 321 331 -50 64 59 5 1.282 62 3 .78 null .358 null
20 260 126 78 45 182 81 240 128 80 46 162 83 0 0 138 64 22 16 82 78 80 75 263 245 2.247 .445 .512 .488 .463 3.103 52 250 .346 .69 80 4270 9210 61 69 339 347 0 162 58 104 .571 164 106 1.753 .657 -.809 -.606

Total number of rows: 37632

Table truncated, full table size 7999 Kbytes.




Supplementary data files not provided
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