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Sample GSM84722 Query DataSets for GSM84722
Status Public on Nov 23, 2005
Title FL17 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 (FL17)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL17)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18871.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 69 65 64 59 5 6 67 62 67 63 3 3 0 0 17 26 19 27 21 21 3 3 11 6 .833 1.2 1 1.384 1.36 2.798 80 436 17.888 .03 100 1290 9450 64 74 40 50 -50 82 75 8 1.519 78 4 .658 1.266 .603 .34
2 71 64 65 60 6 4 70 58 68 64 5 -2 0 0 22 25 19 26 18 18 5 3 10 3 1.5 .667 null 1.376 1.633 3.172 80 387 4.178 .13 100 1450 9450 64 74 56 66 -50 81 76 5 .844 73 null 1.185 null -.245 null
3 971 772 65 59 906 713 1016 568 68 62 951 509 0 0 354 554 20 25 100 98 96 96 1619 1460 1.271 .787 .535 .633 .597 2.483 80 367 .977 .8 100 1620 9450 64 74 73 83 0 977 75 903 .996 719 644 1.004 .678 -.006 -.562
4 1440 334 63 60 1377 274 1705 328 66 62 1642 268 0 0 610 110 21 26 100 97 98 97 1651 1910 5.026 .199 .163 .227 .175 2.429 80 338 .159 .79 100 1760 9460 65 75 87 97 0 423 76 347 .252 415 339 3.97 .207 -1.989 -2.275
5 345 175 64 59 281 116 350 172 67 64 286 113 0 0 143 72 18 26 94 88 88 78 397 399 2.422 .413 .395 .388 .378 3.13 52 313 .291 .61 90 1920 9450 64 73 103 112 0 222 75 147 .523 218 143 1.914 .5 -.936 -1
6 7759 1132 63 63 7696 1069 8721 1119 65 67 8658 1056 0 0 2745 583 18 28 100 98 100 97 8765 9714 7.199 .139 .122 .143 .125 2.389 80 401 .128 .83 100 2080 9450 64 74 119 129 0 1433 80 1353 .176 1416 1337 5.687 .154 -2.508 -2.695
7 346 134 63 62 283 72 340 131 64 67 277 69 0 0 148 49 18 29 96 78 94 57 355 346 3.931 .254 .249 .254 .265 2.511 52 289 .22 .64 90 2230 9450 64 73 134 143 0 170 78 91 .322 166 87 3.105 .315 -1.635 -1.665
8 67 69 63 64 4 5 65 68 65 67 2 4 0 0 18 25 18 29 21 20 3 1 9 6 .8 1.25 2 1.426 1.333 3.55 80 396 17.338 .03 100 2380 9450 64 74 149 159 -50 87 81 6 1.582 86 5 .632 2.532 .662 1.34
9 182 134 66 57 116 77 187 123 70 61 121 66 0 0 71 64 19 26 86 78 84 59 193 187 1.506 .664 .545 .556 .652 3.778 52 313 .763 .62 90 2540 9450 64 73 165 174 0 170 72 97 .84 156 84 1.19 .69 -.251 -.534
10 64 65 61 58 3 7 62 63 64 62 1 5 0 0 19 25 18 26 18 20 6 3 10 6 .429 2.333 5 1.426 1.5 3.936 80 395 -1 -1 100 2690 9440 63 73 180 190 -50 82 73 9 2.954 80 6 .339 6.329 1.562 2.662
11 182 95 63 60 119 35 183 90 64 64 120 30 0 0 70 37 18 27 91 55 87 27 154 150 3.4 .294 .25 .311 .3 3.162 80 389 .198 .34 100 2850 9450 64 74 196 206 0 120 76 44 .372 114 38 2.686 .316 -1.425 -1.66
12 76 64 68 62 8 2 74 64 69 66 6 2 0 0 24 21 20 26 23 11 11 1 10 8 4 .25 .333 .895 .9 3.695 80 380 8.637 .03 100 3010 9440 63 73 212 222 -50 81 78 3 .316 81 3 3.16 .422 -1.66 -1.245
13 221 127 68 63 153 64 217 118 71 69 149 55 0 0 83 48 35 28 92 76 80 48 217 204 2.391 .418 .369 .364 .399 2.521 80 373 .378 .62 100 3170 9450 64 74 228 238 0 161 80 81 .529 149 70 1.889 .467 -.917 -1.098
14 61 63 63 59 -2 4 57 60 67 63 -6 1 0 0 19 27 35 26 3 21 0 6 2 -5 null null null 1.172 1.091 3.304 80 381 .062 .05 100 3320 9440 63 73 243 253 -50 80 75 5 null 76 1 null null null null
15 230 146 65 66 165 80 234 144 68 68 169 78 0 0 82 65 20 28 92 80 88 59 245 247 2.063 .485 .462 .557 .571 2.257 52 348 .487 .66 90 3480 9440 63 72 259 268 0 185 84 101 .614 182 99 1.629 .584 -.704 -.775
16 425 316 69 68 356 248 428 307 72 72 359 239 0 0 251 182 20 29 92 88 92 86 604 598 1.435 .697 .666 .823 .872 2.84 52 259 .645 .78 80 3670 9440 64 72 279 287 0 400 86 314 .882 389 303 1.134 .843 -.181 -.247
17 75 71 71 70 4 1 73 65 74 73 2 -5 0 0 20 29 20 31 17 12 5 3 5 -3 4 .25 null 1.625 1.696 3.401 80 351 .057 .04 100 3790 9440 63 73 290 300 -50 90 89 1 .316 82 null 3.16 null -1.66 null
18 355 288 76 67 279 221 361 281 79 72 285 214 0 0 92 106 24 30 100 98 97 96 500 499 1.262 .792 .751 .752 .779 1.868 80 378 .833 .82 100 3950 9440 63 73 306 316 0 365 85 280 1.003 356 271 .997 .95 .004 -.073
19 83 60 76 68 7 -8 81 59 79 71 5 -9 0 0 21 24 23 29 22 5 2 1 -1 -4 null null null 1.28 1.19 2.901 80 404 .208 .06 100 4100 9440 63 73 321 331 -50 76 86 -10 null 75 null null null null null
20 162 117 70 66 92 51 149 110 73 71 79 44 0 0 91 38 23 30 62 68 53 34 143 123 1.804 .554 .557 .854 .636 4.49 32 155 .45 .6 60 4270 9430 64 70 340 346 0 148 84 65 .702 139 56 1.425 .705 -.511 -.504

Total number of rows: 37632

Table truncated, full table size 7902 Kbytes.




Supplementary data files not provided

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