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Sample GSM84730 Query DataSets for GSM84730
Status Public on Nov 23, 2005
Title FL10 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 (FL10)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL10)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18877.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 60 45 55 41 5 4 58 45 58 46 3 4 0 0 19 15 18 18 23 18 5 1 9 7 1.25 .8 1.333 .898 1.016 3.085 80 415 .633 .14 100 1640 8760 51 61 59 69 -50 49 45 4 .879 49 4 1.138 1.465 -.186 .551
2 60 43 51 40 9 3 56 43 55 44 5 3 0 0 21 16 17 18 28 17 7 2 12 8 3 .333 .6 1.064 1.026 5.111 80 309 .369 .09 100 1800 8760 51 61 75 85 -50 47 44 3 .366 47 3 2.73 .659 -1.449 -.601
3 309 346 55 44 254 302 218 209 58 46 163 165 0 0 203 258 18 18 98 98 90 94 556 328 .841 1.189 1.012 1.149 1.156 2.749 156 682 1.324 .76 150 1930 8780 50 65 85 100 0 380 48 332 1.307 230 181 .765 1.112 .386 .154
4 811 287 57 45 754 242 780 301 60 47 723 256 0 0 414 160 17 16 100 92 100 91 996 979 3.116 .321 .354 .282 .309 3.073 80 359 .276 .77 100 2110 8770 52 62 106 116 0 315 49 266 .353 331 281 2.835 .389 -1.503 -1.362
5 192 138 55 44 137 94 180 133 58 46 125 89 0 0 97 76 18 16 92 80 84 71 231 214 1.457 .686 .712 .65 .736 3.941 52 252 .568 .54 80 2270 8780 54 62 123 131 0 152 48 103 .754 146 98 1.326 .782 -.407 -.354
6 4053 969 56 42 3997 927 3419 871 59 46 3363 829 0 0 2581 634 18 19 100 95 100 93 4924 4192 4.312 .232 .247 .239 .22 3.357 80 388 .186 .77 100 2430 8770 52 62 138 148 0 1065 46 1019 .255 957 911 3.924 .271 -1.972 -1.884
7 157 81 55 41 102 40 154 77 59 44 99 36 0 0 53 36 17 17 92 67 84 51 142 135 2.55 .392 .364 .435 .479 2.984 52 234 .315 .43 80 2580 8780 54 62 154 162 0 89 45 44 .431 85 40 2.321 .4 -1.214 -1.323
8 63 46 58 43 5 3 59 45 60 46 1 2 0 0 20 18 17 18 23 12 12 8 8 3 1.667 .6 2 1.147 .764 4.055 80 394 .988 .09 100 2730 8760 51 61 168 178 -50 51 47 3 .659 49 2 1.517 2.198 -.601 1.136
9 106 120 59 46 47 74 98 124 60 49 39 78 0 0 40 46 18 19 76 90 55 77 121 117 .635 1.574 2 1.639 1.66 3.437 80 344 1.676 .43 100 2890 8780 53 63 184 194 0 132 51 81 1.73 136 86 .578 2.198 .791 1.136
10 58 44 57 45 1 -1 56 41 60 48 -1 -4 0 0 17 18 18 17 13 15 5 3 0 -5 null null null 1.335 1.127 4.423 80 379 3.796 .03 100 3040 8760 51 61 199 209 -50 48 49 -1 null 45 null null null null null
11 187 131 59 46 128 85 191 135 62 48 132 89 0 0 61 51 17 17 95 87 93 81 213 221 1.506 .664 .674 .64 .66 2.388 80 351 .666 .68 100 3210 8770 52 62 216 226 0 144 51 93 .73 148 98 1.37 .741 -.455 -.433
12 67 49 59 42 8 7 63 45 61 48 4 3 0 0 20 22 17 55 27 1 11 0 15 7 1.143 .875 .75 1.3 1.475 4.566 80 362 3.79 .03 100 3350 8760 51 61 230 240 -50 54 46 8 .962 49 3 1.04 .824 -.057 -.279
13 147 100 58 45 89 55 140 105 60 47 82 60 0 0 50 40 17 17 92 80 86 68 144 142 1.618 .618 .732 .672 .683 2.869 80 378 .591 .62 100 3520 8760 51 61 247 257 0 110 49 60 .679 115 66 1.473 .804 -.558 -.315
14 78 55 59 46 19 9 70 53 62 47 11 7 0 0 34 20 17 17 40 28 20 12 28 18 2.111 .474 .636 .885 .931 3.728 80 367 .266 .16 100 3670 8760 51 61 262 272 -50 60 51 10 .521 58 8 1.921 .699 -.942 -.516
15 155 110 63 45 92 65 151 108 64 48 88 63 0 0 52 42 17 18 92 86 86 73 157 151 1.415 .707 .716 .723 .72 2.865 80 331 .543 .51 100 3830 8770 52 62 278 288 0 121 49 71 .776 119 69 1.288 .787 -.365 -.346
16 322 367 64 48 258 319 346 391 66 52 282 343 0 0 153 198 19 23 92 94 89 88 577 625 .809 1.236 1.216 1.246 1.286 2.716 120 419 1.321 .81 120 3980 8770 51 63 292 304 0 403 53 351 1.359 430 377 .736 1.337 .442 .419
17 67 48 64 46 3 2 66 46 67 49 2 0 0 0 18 17 19 21 20 12 3 0 5 2 1.5 .667 null 1.097 1.129 3.964 80 331 -1 -1 100 4130 8760 51 61 308 318 -50 53 51 2 .733 51 0 1.365 null -.449 null
18 210 102 65 49 145 53 200 99 68 51 135 50 0 0 57 34 21 19 96 86 95 67 198 185 2.736 .366 .37 .345 .316 2.508 80 368 .281 .53 100 4280 8770 52 62 323 333 0 112 54 58 .402 109 55 2.49 .407 -1.316 -1.297
19 64 49 64 44 0 5 61 47 67 46 -3 3 0 0 19 17 20 16 13 21 2 5 5 0 null null null .642 .81 4.166 80 394 .115 .04 100 4440 8760 51 61 339 349 -50 54 48 5 null 52 3 null null null null
20 252 103 65 46 187 57 255 103 68 50 190 57 0 0 70 36 21 19 100 81 98 68 244 247 3.281 .305 .3 .275 .289 2.198 80 374 .258 .62 100 4600 8770 52 62 355 365 0 113 51 63 .335 113 63 2.985 .33 -1.578 -1.601

Total number of rows: 37632

Table truncated, full table size 7952 Kbytes.




Supplementary data files not provided
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