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Sample GSM94450 Query DataSets for GSM94450
Status Public on Feb 01, 2006
Title "MA83-1(B) (red, channel 2) vs. MA99-1(A) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA99-1(A) (green)
Organism Caenorhabditis elegans
Characteristics MA99-1(A) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA83-1(B) (red)
Organism Caenorhabditis elegans
Characteristics MA83-1(B) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16492.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 30, 2006
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 GPL2646
Series (1)
GSE4123 The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 2240 3181 71 161 2169 3020 1179 1331 75 166 1108 1170 0 0 2074 3051 23 54 83 85 81 82 5189 2278 .718 1.392 1.056 1.767 1.362 2.263 156 705 1.387 .96 140 2200 18720 78 92 100 114 0 1628 82 1546 .713 681 599 1.403 .541 -.489 -.888
2 989 1583 73 164 916 1419 656 933 76 171 583 769 0 0 864 1365 24 53 82 83 75 78 2335 1352 .646 1.549 1.319 2.21 1.48 2.505 156 499 1.51 .96 140 2370 18710 77 91 117 131 0 810 84 726 .793 478 394 1.261 .675 -.335 -.567
3 397 674 72 165 325 509 309 545 75 169 237 380 0 0 343 512 23 53 75 70 66 61 834 617 .639 1.566 1.603 2.445 1.527 2.986 120 432 1.425 .94 130 2540 18710 77 90 134 147 0 345 84 261 .802 279 195 1.247 .821 -.319 -.285
4 1469 1409 74 167 1395 1242 453 520 76 172 379 353 0 0 1683 1535 22 53 80 79 72 66 2637 732 1.123 .89 .931 2.735 .92 7.077 120 350 .865 .96 120 2700 18730 80 92 151 163 0 721 85 636 .456 266 181 2.194 .477 -1.134 -1.069
5 2838 2651 75 172 2763 2479 1315 995 78 176 1240 823 0 0 3396 3004 22 58 85 78 78 69 5242 2063 1.115 .897 .664 2.989 .844 7.205 120 404 .847 .95 120 2860 18730 80 92 167 179 0 1357 88 1269 .459 509 421 2.177 .34 -1.123 -1.558
6 181 357 76 173 105 184 104 274 79 177 28 101 0 0 206 264 23 60 55 65 33 43 289 129 .571 1.752 3.607 8.16 2.095 15.735 80 357 1.126 .8 100 3010 18720 80 90 183 193 0 183 89 94 .897 140 52 1.115 1.846 -.157 .885
7 1257 2128 76 175 1181 1953 1509 2134 79 177 1433 1959 0 0 920 1552 23 55 86 88 84 83 3134 3392 .605 1.654 1.367 2.076 1.669 2.347 120 532 1.609 .96 130 3180 18720 78 91 198 211 0 1089 90 1000 .846 1092 1003 1.181 .7 -.24 -.515
8 552 823 76 180 476 643 313 640 79 181 237 460 0 0 489 670 22 56 82 72 78 67 1119 697 .74 1.351 1.941 1.571 1.324 1.191 80 293 1.284 .94 110 3340 18730 80 91 215 226 0 421 92 329 .691 328 235 1.446 .993 -.532 -.009
9 9474 7918 76 176 9398 7742 2374 1645 79 181 2298 1469 0 0 11855 9826 23 58 76 73 68 67 17140 3767 1.214 .824 .639 3.011 .858 7.821 208 705 .802 .97 160 3500 18720 77 93 229 245 0 4053 90 3963 .422 842 752 2.372 .327 -1.246 -1.612
10 583 1009 78 170 505 839 538 895 80 178 460 725 0 0 462 719 24 57 83 84 79 74 1344 1185 .602 1.661 1.576 2.839 1.767 4.289 120 353 1.484 .93 130 3670 18720 78 91 247 260 0 516 87 429 .85 458 371 1.176 .807 -.234 -.31
11 2340 4437 77 177 2263 4260 1666 2488 79 184 1589 2311 0 0 1969 3965 23 56 89 86 82 82 6523 3900 .531 1.882 1.454 2.798 1.848 3.886 156 521 1.894 .97 150 3810 18730 78 93 260 275 0 2271 91 2181 .964 1274 1183 1.038 .744 -.054 -.426
12 507 807 75 171 432 636 464 686 77 178 389 515 0 0 380 575 22 53 90 81 84 72 1068 904 .679 1.472 1.324 1.814 1.536 1.208 120 405 1.355 .91 130 3980 18730 79 92 278 291 0 413 88 326 .754 351 264 1.327 .678 -.408 -.561
13 1011 1493 75 176 936 1317 212 352 77 179 137 176 0 0 1534 2158 21 52 69 67 63 59 2253 313 .711 1.407 1.285 2.153 1.39 2.378 120 387 1.349 .96 120 4140 18730 80 92 295 307 0 764 90 674 .72 180 90 1.388 .658 -.473 -.605
14 243 471 74 176 169 295 154 300 76 179 80 124 0 0 208 366 22 53 60 60 57 51 464 204 .573 1.746 1.55 3.779 1.537 9.366 120 422 1.586 .89 120 4300 18720 79 91 311 323 0 241 90 151 .893 154 63 1.119 .793 -.162 -.334
15 250 529 72 180 178 349 173 374 74 184 101 194 0 0 207 426 22 57 65 65 58 55 527 295 .51 1.961 1.921 3.423 1.912 5.648 120 415 1.857 .91 120 4460 18720 79 91 327 339 0 271 92 179 1.004 191 99 .996 .983 .005 -.024
16 617 997 74 187 543 810 692 1055 80 195 618 868 0 0 405 662 29 67 90 80 86 73 1353 1486 .67 1.492 1.405 1.476 1.413 .846 120 458 1.468 .93 130 4610 18730 79 92 341 354 0 510 96 415 .764 540 444 1.31 .719 -.389 -.476
17 2307 2220 76 186 2231 2034 794 962 83 195 718 776 0 0 2831 2551 30 69 71 65 63 62 4265 1494 1.097 .912 1.081 3.505 .992 8.421 120 405 .864 .95 120 4780 18730 80 92 359 371 0 1136 95 1041 .467 492 397 2.143 .553 -1.1 -.854
18 643 1130 73 175 570 955 669 996 76 185 596 821 0 0 494 818 22 57 86 83 79 75 1525 1417 .597 1.675 1.378 2.609 1.664 3.622 120 445 1.592 .95 130 4950 18720 78 91 375 388 0 578 90 489 .858 510 420 1.166 .705 -.222 -.504
19 1059 1640 74 177 985 1463 1239 1804 78 183 1165 1627 0 0 816 1208 23 51 86 84 84 81 2448 2792 .673 1.485 1.397 2.629 1.49 5.571 120 379 1.414 .95 130 5110 18730 79 92 391 404 0 839 91 749 .76 923 833 1.315 .715 -.395 -.484
20 2499 2461 76 183 2423 2278 1791 1541 79 185 1715 1358 0 0 2244 2299 23 53 82 82 78 79 4701 3073 1.064 .94 .792 2.061 .884 7.041 156 478 .958 .97 140 5260 18730 79 93 406 420 0 1260 94 1166 .481 789 695 2.078 .405 -1.055 -1.303

Total number of rows: 21504

Table truncated, full table size 4711 Kbytes.




Supplementary data files not provided
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