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Sample GSM84742 Query DataSets for GSM84742
Status Public on Nov 23, 2005
Title FL22 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 (FL22)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL22)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, Follicular Lymphoma
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24864.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
1 109 100 107 92 2 8 109 95 109 95 2 3 0 0 28 32 27 29 20 21 2 5 10 5 .25 4 1.5 .683 .679 3.608 80 428 5.612 .03 100 2130 8580 45 55 64 74 -50 67 62 5 2.685 64 2 .373 1.007 1.425 .01
2 104 89 103 87 1 2 106 86 105 89 3 -1 0 0 27 27 25 26 12 13 3 5 3 2 .5 2 null .744 .726 4.078 80 379 6.435 .03 100 2280 8580 45 55 79 89 -50 60 58 1 1.342 58 null .745 null .425 null
3 556 873 104 85 452 788 554 892 105 89 450 807 0 0 188 303 25 27 98 98 96 98 1240 1257 .574 1.743 1.793 1.809 1.725 1.416 80 402 1.738 .95 110 2450 8600 46 57 95 106 0 586 57 529 1.17 599 542 .855 1.204 .227 .267
4 1603 1008 103 85 1500 923 1598 973 109 102 1495 888 0 0 538 310 48 130 100 100 97 97 2423 2383 1.625 .615 .594 .635 .616 1.422 80 405 .608 .92 110 2610 8590 45 56 111 122 0 677 57 619 .413 653 596 2.421 .399 -1.276 -1.327
5 239 217 102 89 137 128 237 215 109 105 135 126 0 0 87 71 50 137 81 38 67 2 265 261 1.07 .934 .933 .951 .872 1.916 80 365 .931 .73 110 2760 8600 46 57 126 137 0 146 60 86 .627 144 85 1.595 .626 -.673 -.675
6 7143 2388 103 91 7040 2297 7482 2407 105 95 7379 2316 0 0 2161 575 27 38 100 100 100 100 9337 9695 3.065 .326 .314 .338 .337 1.268 80 403 .309 .97 110 2910 8590 45 56 141 152 0 1603 61 1542 .219 1615 1554 4.567 .211 -2.191 -2.247
7 242 155 99 90 143 65 232 141 101 95 133 51 0 0 88 60 26 40 96 59 88 36 208 184 2.2 .455 .383 .483 .546 2.751 52 283 .431 .59 90 3070 8590 46 55 158 167 0 104 60 44 .305 95 34 3.278 .257 -1.713 -1.958
8 106 111 98 90 8 21 107 102 100 92 9 12 0 0 25 36 24 28 31 36 5 15 29 21 .381 2.625 1.333 1.09 1.192 4.878 80 376 9.502 .05 100 3220 8580 45 55 173 183 -50 74 60 14 1.762 68 8 .568 .895 .817 -.16
9 153 197 101 92 52 105 147 193 104 95 46 101 0 0 43 58 27 27 71 93 40 81 157 147 .495 2.019 2.196 1.921 2 2.654 80 398 2.348 .49 110 3380 8590 45 56 188 199 0 132 62 70 1.355 130 68 .738 1.474 .438 .559
10 111 100 101 94 10 6 111 102 104 97 10 8 0 0 27 25 27 29 25 16 6 1 16 18 1.667 .6 .8 .971 .836 5.392 80 393 -1 -1 100 3530 8580 45 55 204 214 -50 67 63 4 .403 68 5 2.483 .537 -1.312 -.897
11 257 252 100 95 157 157 246 243 104 100 146 148 0 0 100 80 27 35 96 100 90 91 314 294 1 1 1.014 1.052 .944 2.028 80 374 .943 .72 100 3700 8590 46 56 221 231 0 169 64 105 .671 163 99 1.49 .68 -.575 -.556
12 120 104 100 90 20 14 118 96 104 98 18 6 0 0 40 36 27 48 28 17 11 1 34 24 1.429 .7 .333 1.12 1.048 3.501 80 398 10.716 .05 100 3840 8580 45 55 235 245 -50 70 60 9 .47 64 4 2.129 .224 -1.09 -2.16
13 198 180 99 88 99 92 190 176 101 93 91 88 0 0 54 43 25 35 91 87 86 70 191 179 1.076 .929 .967 .967 .826 2.2 80 432 .864 .63 110 4010 8590 45 56 251 262 0 121 59 62 .624 118 59 1.603 .649 -.681 -.624
14 120 148 105 99 15 49 114 111 108 105 9 12 0 0 41 101 33 34 30 36 10 21 64 21 .306 3.267 1.333 1.847 1.836 3.682 80 366 3.89 .37 100 4160 8580 45 55 267 277 -50 99 66 33 2.192 74 8 .456 .895 1.133 -.16
15 198 229 111 111 87 118 198 230 116 117 87 119 0 0 55 57 42 36 80 93 51 82 205 206 .737 1.356 1.368 1.332 1.413 2.082 80 421 1.473 .59 110 4320 8590 45 56 282 293 0 154 74 79 .91 154 80 1.099 .918 -.136 -.123
16 455 1518 114 124 341 1394 454 1534 117 127 340 1410 0 0 113 455 29 41 100 100 100 100 1735 1750 .245 4.088 4.147 4.1 3.891 1.6 80 390 4.449 .89 110 4480 8580 44 55 298 309 0 1019 83 936 2.744 1030 946 .364 2.783 1.456 1.477
17 109 110 111 115 -2 -5 107 103 113 119 -4 -12 0 0 28 36 29 41 13 11 2 2 -7 -16 null null null 1.079 1.211 4.249 80 373 5.93 .09 100 4620 8580 45 55 313 323 -50 74 77 -3 null 69 null null null null null
18 282 202 107 100 175 102 284 196 109 102 177 96 0 0 67 53 28 34 98 92 96 67 277 273 1.716 .583 .542 .52 .536 2.1 52 324 .507 .67 90 4790 8570 44 53 330 339 0 136 67 68 .391 132 64 2.556 .364 -1.354 -1.458
19 109 101 106 98 3 3 108 101 108 101 2 3 0 0 28 27 29 30 17 16 3 2 6 5 1 1 1.5 1.004 .833 3.638 80 406 -1 -1 100 4940 8570 44 54 345 355 -50 68 66 2 .671 68 2 1.49 1.007 -.575 .01
20 348 265 105 103 243 162 339 266 108 105 234 163 0 0 89 72 29 31 100 98 98 92 405 397 1.5 .667 .697 .634 .671 1.762 52 301 .651 .77 90 5100 8580 45 54 361 370 0 178 69 109 .447 179 109 2.235 .468 -1.16 -1.097

Total number of rows: 37632

Table truncated, full table size 7944 Kbytes.




Supplementary data files not provided
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