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Sample GSM84734 Query DataSets for GSM84734
Status Public on Nov 23, 2005
Title FL21 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 (FL21)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL21)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, Follicular Lymphoma
Image: http://smd.stanford.edu/MicroArray/gifs/2002-02/24902.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
1 105 103 100 92 5 11 103 96 104 95 3 4 0 0 24 46 30 31 15 22 1 8 16 7 .455 2.2 1.333 1.554 1.457 3.223 80 408 -1 -1 100 1850 8930 48 58 44 54 -50 123 110 13 2.619 114 5 .382 1.587 1.389 .667
2 107 101 100 89 7 12 103 93 102 92 3 4 0 0 24 39 26 32 22 21 3 8 19 7 .583 1.714 1.333 1.027 1 3.96 80 385 5.541 .12 100 2000 8930 48 58 59 69 -50 120 106 14 2.041 111 5 .49 1.587 1.029 .667
3 454 437 101 88 353 349 454 427 103 90 353 339 0 0 157 155 25 28 98 100 97 97 702 692 1.011 .989 .96 .982 .932 1.657 80 363 .98 .89 100 2170 8940 49 59 76 86 0 520 105 415 1.177 508 404 .85 1.143 .235 .193
4 1008 692 101 89 907 603 1012 687 103 91 911 598 0 0 322 244 24 29 100 98 100 98 1510 1509 1.504 .665 .656 .647 .651 1.333 80 360 .647 .93 100 2330 8930 48 58 92 102 0 824 106 718 .791 818 712 1.263 .781 -.337 -.356
5 202 159 104 90 98 69 195 142 105 93 91 52 0 0 62 92 25 30 90 70 80 37 167 143 1.42 .704 .571 .66 .703 3.101 80 403 1.069 .35 110 2480 8930 47 58 106 117 0 189 107 82 .838 169 62 1.193 .68 -.255 -.556
6 4690 2220 101 86 4589 2134 4622 2276 103 91 4521 2190 0 0 1568 554 25 29 100 100 100 100 6723 6711 2.15 .465 .484 .486 .484 1.351 80 400 .435 .96 110 2630 8940 48 59 121 132 0 2643 102 2540 .554 2710 2607 1.806 .577 -.853 -.794
7 218 142 97 89 121 53 211 138 100 90 114 49 0 0 65 46 24 28 94 71 86 34 174 163 2.283 .438 .43 .467 .419 2.926 52 324 .33 .4 90 2790 8930 48 57 138 147 0 169 106 63 .521 164 58 1.918 .512 -.939 -.967
8 115 127 96 90 19 37 109 98 99 93 13 8 0 0 36 97 25 28 32 36 12 17 56 21 .514 1.947 .615 1.442 1.188 5.047 80 425 5.75 .26 100 2950 8930 48 58 154 164 -50 151 107 44 2.318 117 10 .431 .733 1.213 -.449
9 148 114 101 97 47 17 142 107 107 102 41 10 0 0 36 31 33 34 58 16 25 16 64 51 2.765 .362 .244 .342 .225 3.249 12 94 1.415 .19 50 3070 8950 52 57 168 173 0 136 115 20 .431 127 12 2.322 .29 -1.216 -1.784
10 111 113 99 94 12 19 103 104 102 95 4 10 0 0 50 47 27 29 25 32 11 15 31 14 .632 1.583 2.5 .889 .896 4.201 80 451 1.344 .23 100 3260 8920 47 57 185 195 -50 135 112 23 1.885 124 12 .531 2.976 .915 1.573
11 178 152 101 91 77 61 179 154 103 94 78 63 0 0 52 43 26 29 82 72 67 53 138 141 1.262 .792 .808 .866 .853 2.392 80 415 .783 .5 110 3420 8930 47 58 200 211 0 181 108 73 .943 183 75 1.06 .962 -.085 -.057
12 101 106 100 89 1 17 100 102 102 94 0 13 0 0 28 40 27 30 12 30 3 12 18 13 .059 17 null 1.784 1.909 3.777 80 364 4.638 .08 100 3570 8920 47 57 216 226 -50 126 106 20 20.238 121 15 .049 null 4.339 null
13 170 114 96 87 74 27 172 113 100 92 76 26 0 0 53 31 26 29 82 45 62 17 101 102 2.741 .365 .342 .433 .47 3.149 80 399 .262 .26 100 3730 8930 48 58 232 242 0 136 104 32 .434 135 31 2.302 .407 -1.203 -1.296
14 113 124 97 91 16 33 103 102 98 95 6 11 0 0 48 100 23 29 28 27 10 11 49 17 .485 2.063 1.833 2.217 2.125 3.72 80 393 3.35 .4 100 3890 8920 47 57 248 258 -50 148 108 39 2.455 121 13 .407 2.183 1.296 1.126
15 157 126 98 93 59 33 152 118 99 95 54 25 0 0 49 41 24 31 76 40 53 21 92 79 1.788 .559 .463 .508 .597 3.065 52 324 .678 .35 90 4050 8930 48 57 264 273 0 150 111 39 .666 140 30 1.502 .551 -.587 -.859
16 259 210 97 93 162 117 264 213 99 95 167 120 0 0 80 58 24 29 96 96 92 82 279 287 1.385 .722 .719 .689 .756 1.8 80 397 .667 .69 100 4210 8930 48 58 280 290 0 250 111 139 .86 254 143 1.163 .855 -.218 -.225
17 101 89 96 90 5 -1 99 85 98 93 3 -5 0 0 25 30 24 29 20 12 7 5 4 -2 null null null 1.097 1.011 4.282 80 379 -1 -1 100 4360 8920 47 57 295 305 -50 106 107 -1 null 101 null null null null null
18 262 123 92 91 170 32 264 117 97 94 172 26 0 0 61 43 25 31 100 45 98 23 202 198 5.313 .188 .151 .21 .223 2.489 80 394 .158 .31 100 4520 8920 47 57 311 321 0 146 108 38 .224 139 31 4.463 .18 -2.158 -2.474
19 94 85 95 89 -1 -4 91 84 97 92 -4 -5 0 0 21 28 24 28 8 12 2 2 -5 -9 null null null 1.311 1.542 3.44 80 379 -1 -1 100 4670 8920 47 57 326 336 -50 101 106 -5 null 100 null null null null null
20 311 115 97 90 214 25 309 106 99 94 212 16 0 0 85 42 25 27 100 40 97 21 239 228 8.56 .117 .075 .166 .179 2.069 80 373 .129 .39 100 4830 8930 48 58 342 352 0 137 107 30 .139 126 19 7.19 .09 -2.846 -3.476

Total number of rows: 37632

Table truncated, full table size 7860 Kbytes.




Supplementary data files not provided
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