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Sample GSM84716 Query DataSets for GSM84716
Status Public on Nov 23, 2005
Title Normal Tonsil (N1)
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Normal Tonsil (N1)
Organism Homo sapiens
Characteristics Normal Tonsil (N1)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Lymphoma Classification, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12507.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 GPL3042
Series (2)
GSE3646 Follicular lymphoma and normal lymphoid tissue comparisons
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
1 415 428 76 67 339 361 361 433 83 75 285 366 0 0 282 285 51 57 78 77 71 73 700 651 .939 1.065 1.284 1.237 1.338 3.514 80 437 1.115 .69 100 1550 8110 158 168 22 32 0 586 92 495 1.459 593 501 .686 1.759 .545 .815
2 293 165 73 62 220 103 176 101 75 63 103 39 0 0 270 134 14 18 93 62 84 53 323 142 2.136 .468 .379 .45 .384 3.001 32 213 .368 .63 70 1690 8090 157 164 37 44 0 226 85 141 .641 138 53 1.559 .519 -.641 -.947
3 2277 629 73 64 2204 565 2210 535 75 69 2137 471 0 0 945 360 17 24 100 100 100 96 2769 2608 3.901 .256 .22 .208 .229 1.958 32 199 .244 .82 70 1830 8090 157 164 51 58 0 862 88 774 .351 733 645 2.848 .302 -1.51 -1.728
4 112 86 75 68 37 18 82 74 82 80 7 6 0 0 85 50 40 81 20 10 13 2 55 13 2.056 .486 .857 1.028 .955 3.277 80 396 1.431 .25 100 1960 8080 155 165 63 73 -50 118 93 25 .666 101 8 1.501 1.174 -.585 .232
5 997 272 77 66 920 206 958 260 87 91 881 194 0 0 423 136 50 115 100 68 100 40 1126 1075 4.466 .224 .22 .192 .195 1.966 32 175 .226 .51 70 2100 8090 157 164 78 85 0 373 90 282 .307 356 266 3.26 .302 -1.705 -1.729
6 117 93 78 68 39 25 82 76 83 72 4 8 0 0 101 53 26 27 21 27 20 16 64 12 1.56 .641 2 .752 .74 4.908 80 394 .339 .35 100 2230 8080 155 165 90 100 -50 127 93 34 .878 104 11 1.139 2.74 -.188 1.454
7 624 356 76 64 548 292 498 236 78 67 422 172 0 0 468 300 18 17 94 92 90 90 840 594 1.877 .533 .408 .576 .533 4.382 52 249 .484 .71 80 2380 8100 158 166 106 114 0 488 88 400 .73 323 236 1.37 .558 -.454 -.841
8 443 276 75 63 368 213 416 246 77 67 341 183 0 0 258 156 16 21 92 90 88 82 581 524 1.728 .579 .537 .604 .596 3.495 52 250 .5 .72 80 2520 8100 158 166 120 128 0 378 86 292 .793 337 251 1.261 .735 -.335 -.444
9 441 155 82 63 359 92 418 134 84 66 336 71 0 0 217 71 20 19 100 100 100 58 451 407 3.902 .256 .211 .237 .284 1.848 12 98 .239 .64 50 2640 8100 159 164 133 138 0 212 86 126 .351 184 97 2.849 .289 -1.51 -1.789
10 294 255 84 69 210 186 261 222 84 71 177 153 0 0 139 107 17 21 100 96 93 93 396 330 1.129 .886 .864 1.03 .937 2.483 32 204 .804 .74 70 2780 8100 158 165 146 153 0 349 95 255 1.213 304 210 .824 1.184 .279 .244
11 773 892 84 68 689 824 408 540 84 72 324 472 0 0 847 904 19 23 90 98 88 90 1513 796 .836 1.196 1.457 1.16 1.676 4.081 52 229 1.139 .76 80 2920 8100 158 166 160 168 0 1222 93 1129 1.638 740 647 .61 1.996 .712 .997
12 147 110 79 69 68 41 90 78 83 73 11 9 0 0 170 94 25 23 30 33 21 22 109 20 1.659 .603 .818 .886 .833 4.549 80 377 .393 .53 100 3040 8080 155 165 171 181 -50 151 95 56 .826 107 12 1.211 1.121 -.276 .165
13 386 297 78 69 308 228 386 284 85 75 308 215 0 0 195 126 31 26 100 100 87 96 536 523 1.351 .74 .698 .828 .917 2.451 32 195 .643 .74 70 3190 8100 158 165 187 194 0 407 95 312 1.014 389 295 .986 .956 .02 -.065
14 1011 372 82 68 929 304 1225 414 81 73 1143 346 0 0 439 161 18 19 100 93 100 87 1233 1489 3.056 .327 .303 .316 .322 3.081 32 160 .262 .76 60 3320 8100 159 165 201 207 0 510 93 416 .448 567 474 2.231 .415 -1.158 -1.27
15 542 283 83 73 459 210 441 253 83 75 358 180 0 0 322 149 16 20 100 91 100 83 669 538 2.186 .458 .503 .55 .948 3.336 12 104 .319 .59 50 3460 8090 158 163 215 220 0 388 100 288 .627 347 247 1.596 .689 -.674 -.538
16 1931 1079 79 73 1852 1006 2020 1199 81 77 1941 1126 0 0 483 434 17 21 100 100 100 100 2858 3067 1.841 .543 .58 .448 .593 2.475 32 224 .534 .81 70 3590 8090 157 164 227 234 0 1478 100 1378 .744 1642 1542 1.344 .795 -.426 -.332
17 549 371 82 77 467 294 517 331 91 120 435 254 0 0 286 255 62 374 100 34 93 6 761 689 1.588 .63 .584 .497 .665 2.711 32 166 5.163 .26 60 3730 8090 158 164 242 248 0 508 105 403 .862 453 348 1.16 .8 -.214 -.322
18 925 320 82 79 843 241 970 327 85 80 888 248 0 0 272 87 18 19 100 100 100 100 1084 1136 3.498 .286 .279 .283 .288 1.626 32 218 .245 .84 70 3860 8090 157 164 254 261 0 438 108 330 .392 448 340 2.553 .383 -1.352 -1.386
19 384 176 81 72 303 104 393 174 82 73 312 102 0 0 65 55 17 19 100 90 100 84 407 414 2.913 .343 .327 .298 .331 2.164 32 218 .345 .68 70 4000 8090 157 164 268 275 0 241 99 142 .47 238 140 2.127 .448 -1.089 -1.159
20 1225 846 81 76 1144 770 1219 903 83 76 1138 827 0 0 457 443 18 20 100 100 100 100 1914 1965 1.486 .673 .727 .524 .607 2.4 32 218 .706 .86 70 4130 8090 157 164 281 288 0 1159 104 1055 .922 1237 1133 1.085 .995 -.117 -.007

Total number of rows: 39168

Table truncated, full table size 8581 Kbytes.




Supplementary data files not provided
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