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Sample GSM84732 Query DataSets for GSM84732
Status Public on Nov 23, 2005
Title FL5 CR 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 (FL5)
Organism Homo sapiens
Characteristics Follicular lymphoma (FL5)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18879.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 95 73 83 59 12 14 89 63 104 84 6 4 0 0 33 43 342 150 0 1 0 0 26 10 .857 1.167 .667 1 .892 4.778 80 409 16.351 .09 100 1350 8760 59 69 46 56 -50 74 60 14 1.19 64 4 .84 .68 .252 -.556
2 94 90 86 59 8 31 84 59 166 92 -2 0 0 0 40 152 1032 197 0 2 0 2 39 -2 .258 3.875 null .797 .714 3.172 80 366 .108 .53 100 1500 8760 59 69 61 71 -50 92 60 32 3.954 60 0 .253 null 1.983 null
3 1242 846 87 62 1155 784 1307 898 119 90 1220 836 0 0 687 513 117 100 95 92 88 83 1939 2056 1.473 .679 .685 .672 .699 2.241 80 312 .682 .85 100 1660 8760 59 69 77 87 -50 863 63 800 .693 916 853 1.444 .699 -.53 -.516
4 1715 501 87 57 1628 444 1308 374 105 78 1221 317 0 0 1514 400 89 91 78 70 75 62 2072 1538 3.667 .273 .26 .33 .276 3.215 156 578 .237 .86 140 1800 8770 58 72 89 103 0 511 58 453 .278 382 323 3.593 .265 -1.845 -1.916
5 477 352 89 59 388 293 460 350 92 69 371 291 0 0 214 139 28 68 93 90 90 87 681 662 1.324 .755 .784 .813 .743 2.496 80 332 .651 .77 100 1980 8770 60 70 109 119 0 359 60 299 .771 357 297 1.298 .8 -.376 -.321
6 11061 3949 99 66 10962 3883 11783 4130 105 79 11684 4064 0 0 4641 1405 41 61 100 100 100 100 14845 15748 2.823 .354 .348 .39 .331 1.943 80 373 .311 .89 110 2130 8770 59 70 123 134 0 4030 67 3962 .361 4214 4147 2.767 .355 -1.468 -1.494
7 645 269 96 58 549 211 614 249 103 74 518 191 0 0 360 130 41 72 93 83 91 70 760 709 2.602 .384 .369 .422 .387 2.485 80 357 .328 .72 100 2290 8760 59 69 140 150 0 274 59 215 .392 254 195 2.55 .376 -1.35 -1.41
8 81 53 86 48 -5 5 78 47 89 58 -8 -1 0 0 27 34 26 53 8 1 1 1 0 -9 null null null .774 .735 3.487 80 381 10.269 .08 100 2440 8750 58 68 155 165 -50 54 49 5 null 48 null null null null null
9 281 251 86 48 195 203 287 253 89 56 201 205 0 0 106 93 25 41 95 93 91 92 398 406 .961 1.041 1.02 .99 .921 2.189 80 346 .972 .77 100 2600 8770 60 70 171 181 0 256 49 207 1.062 258 209 .941 1.041 .087 .058
10 101 90 85 48 16 42 90 59 89 58 5 11 0 0 45 112 26 92 30 10 8 8 58 16 .381 2.625 2.2 .851 .761 3.642 80 369 7.755 .19 100 2750 8750 58 68 186 196 -50 92 49 43 2.679 60 11 .373 2.245 1.421 1.167
11 289 159 81 45 208 114 305 155 84 58 224 110 0 0 115 62 26 160 90 18 86 0 322 334 1.825 .548 .491 .53 .494 1.915 80 371 4.165 .27 100 2910 8760 59 69 202 212 0 162 46 116 .559 158 112 1.788 .501 -.838 -.997
12 85 50 83 47 2 3 85 47 86 61 2 0 0 0 22 17 28 159 8 0 3 0 5 2 .667 1.5 null .761 .75 3.849 80 380 .368 .18 100 3070 8750 58 68 218 228 -50 51 48 3 1.531 48 0 .653 null .614 null
13 333 209 84 49 249 160 349 225 88 53 265 176 0 0 133 89 35 29 90 86 88 81 409 441 1.556 .643 .664 .545 .612 2.306 80 358 .596 .83 100 3230 8760 59 69 234 244 0 213 50 163 .656 230 180 1.525 .678 -.609 -.561
14 88 72 81 47 7 25 87 55 85 58 6 8 0 0 31 113 26 76 21 5 2 1 32 14 .28 3.571 1.333 .606 .722 3.872 80 366 53.478 .04 100 3380 8750 58 68 249 259 -50 73 48 26 3.644 56 8 .274 1.361 1.866 .444
15 311 261 83 48 228 213 317 268 87 60 234 220 0 0 114 83 25 79 93 91 88 77 441 454 1.07 .934 .94 .947 .923 2.067 80 387 .847 .79 100 3540 8760 59 69 265 275 0 266 49 217 .953 273 224 1.049 .959 -.069 -.06
16 1153 1225 83 47 1070 1178 1219 1330 86 54 1136 1283 0 0 811 823 24 38 90 93 87 91 2248 2419 .908 1.101 1.129 1.208 1.1 2.391 80 356 1.07 .9 100 3710 8760 59 69 282 292 0 1250 48 1202 1.123 1357 1309 .89 1.152 .168 .205
17 92 80 84 47 8 33 88 52 86 51 4 5 0 0 23 125 26 23 25 25 3 11 41 9 .242 4.125 1.25 .986 .824 4.49 80 350 47.978 .05 100 3850 8750 58 68 296 306 -50 82 48 34 4.209 53 5 .238 1.276 2.074 .351
18 337 154 84 49 253 105 348 159 88 53 264 110 0 0 122 64 29 24 92 86 92 76 358 374 2.41 .415 .417 .388 .419 2.347 80 358 .392 .67 100 4010 8760 59 69 312 322 0 157 50 107 .423 162 112 2.361 .425 -1.24 -1.234
19 87 51 85 48 2 3 85 47 88 51 0 -1 0 0 25 22 27 19 15 16 2 7 5 -1 .667 1.5 null .815 .857 3.767 80 377 .187 .12 100 4160 8750 58 68 327 337 -50 52 49 3 1.531 48 null .653 null .614 null
20 348 171 79 46 269 125 342 153 84 50 263 107 0 0 129 88 25 17 97 90 93 86 394 370 2.152 .465 .407 .403 .397 2.357 80 365 .434 .73 100 4330 8750 58 68 344 354 0 174 47 128 .474 156 109 2.109 .415 -1.077 -1.268

Total number of rows: 37632

Table truncated, full table size 8044 Kbytes.




Supplementary data files not provided
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