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Sample GSM84740 Query DataSets for GSM84740
Status Public on Nov 23, 2005
Title FL8 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 (FL8)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL8)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18730.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 72 70 67 66 5 4 73 67 77 69 6 1 0 0 18 28 78 23 0 20 0 6 9 7 1.25 .8 .167 1.385 1.609 3.358 80 429 8.42 .05 100 1540 9060 89 99 53 63 -50 83 79 5 .952 80 1 1.05 .198 -.07 -2.333
2 72 76 70 65 2 11 69 73 72 68 -1 8 0 0 22 27 21 25 23 26 5 5 13 7 .182 5.5 null 1.162 1.31 3.141 80 379 7.17 .04 100 1700 9060 89 99 69 79 -50 90 77 13 6.548 87 10 .153 null 2.711 null
3 1090 1002 70 64 1020 938 1112 1079 73 66 1042 1015 0 0 289 372 22 22 100 100 100 100 1958 2057 1.087 .92 .974 .858 .954 1.845 80 397 .979 .85 110 1860 9070 89 100 84 95 0 1193 76 1117 1.095 1285 1208 .913 1.16 .131 .214
4 1564 509 68 66 1496 443 1644 522 72 72 1576 456 0 0 490 183 38 45 100 95 100 93 1939 2032 3.377 .296 .289 .284 .29 2.431 80 415 .254 .73 110 2010 9070 89 100 99 110 0 606 79 527 .353 621 543 2.837 .344 -1.504 -1.538
5 436 231 69 65 367 166 451 234 74 73 382 169 0 0 152 91 40 48 97 85 93 77 533 551 2.211 .452 .442 .442 .431 2.693 80 369 .384 .64 100 2180 9070 90 100 117 127 0 275 77 198 .538 279 201 1.857 .527 -.893 -.925
6 8796 1867 68 66 8728 1801 9536 2075 71 69 9468 2009 0 0 2764 746 21 23 100 98 100 97 10529 11477 4.846 .206 .212 .219 .208 1.794 80 417 .19 .83 110 2330 9070 89 100 131 142 0 2223 79 2144 .246 2470 2392 4.071 .253 -2.025 -1.985
7 365 177 65 65 300 112 367 173 68 67 302 108 0 0 122 58 20 24 100 96 96 86 412 410 2.679 .373 .358 .384 .342 2.06 52 302 .35 .74 90 2490 9070 90 99 148 157 0 211 77 133 .444 206 129 2.25 .426 -1.17 -1.232
8 73 71 73 64 0 7 71 68 75 68 -2 4 0 0 20 25 22 25 11 22 3 3 7 2 null null null 1.251 1.607 4.209 80 380 -1 -1 100 2640 9060 89 99 163 173 -50 85 76 8 null 81 5 null null null null
9 209 291 74 67 135 224 224 305 76 70 150 238 0 0 80 100 20 25 83 97 82 96 359 388 .603 1.659 1.587 1.688 1.67 2.074 80 376 1.668 .75 110 2800 9080 90 101 178 189 0 346 80 267 1.975 363 283 .506 1.889 .982 .918
10 75 72 71 68 4 4 74 68 73 69 3 0 0 0 25 23 20 22 18 21 6 5 8 3 1 1 null .985 1.1 4.03 80 379 .226 .04 100 2950 9060 89 99 194 204 -50 86 81 5 1.19 81 0 .84 null .252 null
11 242 213 70 67 172 146 250 202 72 71 180 135 0 0 91 86 20 25 92 91 90 85 318 315 1.178 .849 .75 .873 .881 2.858 80 364 .81 .7 100 3120 9070 90 100 211 221 0 254 80 174 1.011 240 161 .99 .893 .015 -.163
12 79 70 72 67 7 3 79 67 75 71 7 0 0 0 23 28 20 25 32 16 8 7 10 7 2.333 .429 null 1.101 1.143 3.184 80 355 1.915 .12 100 3260 9070 90 100 225 235 -50 83 80 4 .51 80 0 1.96 null -.971 null
13 329 299 75 68 254 231 323 311 77 69 248 243 0 0 123 135 21 22 98 91 92 88 485 491 1.1 .909 .98 .81 .9 2.727 80 385 .966 .8 100 3430 9070 90 100 242 252 0 356 81 275 1.083 370 289 .924 1.166 .115 .222
14 68 72 73 68 -5 4 63 72 75 68 -10 4 0 0 21 25 23 22 11 20 5 6 -1 -6 null null null 1.181 1 3.147 80 359 -1 -1 100 3580 9070 90 100 257 267 -50 86 81 5 null 86 5 null null null null
15 336 320 76 68 260 252 350 320 80 71 274 252 0 0 164 118 24 25 90 97 83 96 512 526 1.032 .969 .92 1.132 .92 2.583 80 389 .857 .81 100 3740 9080 91 101 273 283 0 381 81 300 1.154 381 300 .867 1.095 .206 .131
16 600 724 77 68 523 656 440 509 81 72 363 441 0 0 469 591 32 26 85 96 80 90 1179 804 .797 1.254 1.215 1.409 1.232 3.791 80 308 1.332 .8 100 3930 9090 92 102 292 302 -100 862 81 781 1.493 606 525 .67 1.446 .578 .532
17 76 66 74 65 2 1 73 62 78 70 -1 -3 0 0 20 23 26 26 12 18 0 1 3 -4 2 .5 null 2.018 1.789 3.878 80 326 .53 .07 100 4050 9070 90 100 304 314 -50 79 77 1 .595 74 null 1.68 null -.748 null
18 384 413 71 67 313 346 422 421 74 69 351 354 0 0 147 157 28 25 97 100 93 96 659 705 .905 1.105 1.009 1.143 1.093 2.506 80 411 1.137 .79 100 4210 9070 90 100 320 330 0 492 80 412 1.316 501 421 .76 1.201 .396 .264
19 76 75 72 69 4 6 72 71 75 74 0 2 0 0 19 29 24 43 15 8 1 1 10 2 .667 1.5 null 1.144 1.233 3.251 80 399 7.574 .04 100 4360 9070 90 100 335 345 -50 89 82 7 1.786 85 2 .56 null .837 null
20 181 154 71 70 110 84 155 153 75 79 84 83 0 0 104 60 35 58 75 59 57 32 194 167 1.31 .764 .988 .879 .745 3.935 52 265 .973 .45 80 4530 9060 90 98 353 361 0 183 83 100 .909 182 99 1.1 1.176 -.138 .234

Total number of rows: 37632

Table truncated, full table size 8114 Kbytes.




Supplementary data files not provided

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