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Sample GSM84729 Query DataSets for GSM84729
Status Public on Nov 23, 2005
Title FL14 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 (FL14)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL14)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18876.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 83 60 81 56 2 4 79 57 83 58 -2 1 0 0 28 17 25 20 23 17 6 2 6 -1 .5 2 null .639 .724 4.225 80 414 12.078 .04 100 1530 8830 58 68 48 58 -50 71 66 5 2.353 67 1 .425 null 1.234 null
2 78 54 82 54 -4 0 76 51 89 61 -6 -3 0 0 26 17 36 34 8 3 2 0 -4 -9 null null null .63 .55 3.728 80 379 .413 .29 100 1690 8830 58 68 64 74 -50 64 64 0 null 60 null null null null null
3 719 619 85 56 634 563 796 668 100 70 711 612 0 0 306 286 53 48 97 92 91 90 1197 1323 1.126 .888 .861 .856 .909 2.462 80 360 .883 .88 100 1840 8840 59 69 79 89 0 728 66 662 1.045 786 720 .957 1.013 .063 .018
4 1529 795 79 55 1450 740 1644 823 89 64 1565 768 0 0 472 181 41 37 100 100 100 100 2190 2333 1.959 .51 .491 .539 .479 1.683 80 394 .436 .86 110 2000 8850 59 70 94 105 0 935 65 871 .6 968 904 1.666 .577 -.736 -.793
5 304 173 79 51 225 122 300 175 82 54 221 124 0 0 102 75 24 20 95 91 92 85 347 345 1.844 .542 .561 .503 .536 2.286 80 404 .513 .69 110 2160 8840 58 69 110 121 0 204 60 144 .638 206 146 1.568 .66 -.649 -.599
6 7673 2917 79 55 7594 2862 8294 3034 83 58 8215 2979 0 0 2357 839 26 20 100 100 100 100 10456 11194 2.653 .377 .363 .387 .378 1.594 80 395 .344 .91 110 2310 8850 59 70 125 136 0 3432 65 3367 .443 3569 3505 2.255 .427 -1.173 -1.229
7 462 218 79 53 383 165 438 221 82 56 359 168 0 0 217 93 23 18 94 94 92 90 548 527 2.321 .431 .468 .431 .409 2.16 52 302 .383 .82 90 2470 8840 59 68 142 151 0 256 62 194 .507 260 198 1.973 .551 -.98 -.861
8 89 55 84 55 5 0 85 53 86 57 1 -2 0 0 23 19 24 19 17 15 3 5 5 -1 null null null 1.037 1.174 4.372 80 394 7.413 .06 100 2620 8830 58 68 157 167 -50 65 65 0 null 62 null null null null null
9 212 181 83 56 129 125 215 181 88 57 132 125 0 0 72 55 26 19 95 96 81 92 254 257 1.032 .969 .947 1.027 1.019 2.659 80 353 .852 .68 100 2780 8850 60 70 173 183 0 213 66 147 1.14 213 147 .877 1.114 .189 .156
10 85 61 83 55 2 6 81 57 87 57 -2 2 0 0 28 25 25 19 16 26 8 13 8 0 .333 3 null 1.003 1 3.494 80 369 3.741 .08 100 2930 8830 58 68 188 198 -50 72 65 7 3.529 67 2 .283 null 1.819 null
11 277 146 88 60 189 86 293 151 89 61 205 91 0 0 83 47 24 19 95 92 92 83 275 296 2.198 .455 .444 .463 .473 2.188 80 350 .425 .75 100 3090 8840 59 69 204 214 0 172 71 101 .535 178 107 1.868 .522 -.902 -.937
12 86 58 86 56 0 2 80 54 88 60 -6 -2 0 0 26 20 24 21 18 17 7 2 2 -8 null null null .895 .745 3.698 80 362 .156 .1 100 3240 8830 58 68 219 229 -50 68 66 2 null 64 null null null null null
13 317 173 85 56 232 117 321 176 87 60 236 120 0 0 104 72 24 23 97 87 97 83 349 356 1.983 .504 .508 .453 .481 2.329 80 418 .481 .77 100 3410 8840 59 69 236 246 0 204 66 138 .593 207 141 1.685 .598 -.753 -.741
14 161 134 89 54 72 80 125 126 108 59 36 72 0 0 120 52 132 26 16 83 8 58 152 108 .9 1.111 2 1.241 1.3 2.81 12 104 .219 .41 50 3550 8840 61 66 252 257 0 158 64 94 1.307 148 85 .765 2.353 .386 1.234
15 256 164 80 55 176 109 250 163 86 58 170 108 0 0 91 64 66 20 87 91 65 83 285 278 1.615 .619 .635 .591 .671 2.443 80 473 .547 .66 110 3710 8830 57 68 265 276 0 193 65 128 .729 192 127 1.372 .747 -.457 -.42
16 748 724 80 56 668 668 812 715 82 59 732 659 0 0 258 243 24 20 98 100 98 100 1336 1391 1 1 .9 1.037 .988 1.777 80 421 .995 .9 110 3870 8830 57 68 281 292 0 852 66 786 1.176 841 775 .85 1.059 .234 .083
17 85 58 82 54 3 4 81 57 86 57 -1 3 0 0 22 15 25 19 16 11 3 3 7 2 .75 1.333 null .559 .613 3.039 80 379 -1 -1 100 4020 8820 57 67 297 307 -50 68 64 5 1.569 67 4 .638 null .65 null
18 326 120 85 54 241 66 318 126 88 58 233 72 0 0 94 42 25 20 96 83 96 71 307 305 3.652 .274 .309 .246 .285 2.16 80 378 .246 .67 100 4180 8820 57 67 313 323 0 141 64 78 .322 148 85 3.104 .364 -1.634 -1.46
19 84 57 86 56 -2 1 82 55 90 59 -4 -1 0 0 22 20 28 22 10 15 1 5 -1 -5 null null null 1.003 .727 3.688 80 366 18.39 .03 100 4330 8820 57 67 328 338 -50 67 66 1 null 65 null null null null null
20 424 143 85 59 339 84 434 146 90 63 349 87 0 0 124 46 29 23 100 91 100 76 423 436 4.036 .248 .249 .221 .234 2.128 80 343 .226 .74 100 4490 8840 59 69 344 354 0 168 69 99 .292 172 102 3.43 .293 -1.778 -1.77

Total number of rows: 37632

Table truncated, full table size 7932 Kbytes.




Supplementary data files not provided

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