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Sample GSM94461 Query DataSets for GSM94461
Status Public on Feb 01, 2006
Title "MA83-4(A) (red, channel 2) vs. MA41-4(B) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA41-4(B) (green)
Organism Caenorhabditis elegans
Characteristics MA41-4(B) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA83-4(A) (red)
Organism Caenorhabditis elegans
Characteristics MA83-4(A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16496.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 2811 2481 134 237 2677 2244 1554 910 141 242 1420 673 0 0 2762 2487 43 87 87 85 82 77 4921 2093 1.193 .838 .474 1.116 .826 1.314 120 535 .85 .97 120 1050 18620 69 81 64 76 0 1813 173 1640 .613 665 492 1.632 .346 -.707 -1.529
2 1063 1507 136 234 927 1273 1147 1505 142 238 1011 1271 0 0 798 1120 44 89 79 80 75 73 2200 2282 .728 1.373 1.257 2.034 1.444 2.468 120 451 1.328 .95 120 1210 18620 69 81 80 92 0 1101 171 930 1.004 1100 929 .996 .919 .005 -.122
3 492 837 130 216 362 621 477 893 136 225 347 677 0 0 308 422 42 88 81 87 73 82 983 1024 .583 1.715 1.951 3.005 1.811 5.954 80 426 1.308 .83 110 1380 18620 69 80 97 108 0 612 158 454 1.254 653 495 .798 1.426 .326 .512
4 2210 1997 132 217 2078 1780 2734 2315 136 230 2602 2098 0 0 1514 1230 39 92 90 93 87 86 3858 4700 1.167 .857 .806 1.301 .872 1.601 80 416 .803 .96 110 1550 18620 69 80 114 125 0 1460 159 1301 .626 1692 1533 1.597 .589 -.676 -.763
5 6840 3274 140 225 6700 3049 3123 1586 148 235 2983 1361 0 0 7006 3168 56 87 78 77 69 70 9749 4344 2.197 .455 .456 1.682 .477 3.749 120 492 .439 .97 120 1700 18620 69 81 129 141 0 2393 164 2228 .333 1159 995 3.007 .333 -1.588 -1.584
6 452 620 131 214 321 406 220 434 140 224 89 220 0 0 512 544 54 80 72 73 45 60 727 309 .791 1.265 2.472 3.418 1.428 8.005 80 347 .982 .88 100 1870 18620 70 80 147 157 0 453 156 297 .924 317 161 1.082 1.807 -.113 .853
7 1430 1628 126 227 1304 1401 1431 1876 130 239 1305 1649 0 0 976 1162 40 87 89 82 82 79 2705 2954 .931 1.074 1.264 1.75 1.074 5.3 156 583 1.078 .95 140 2020 18620 68 82 160 174 0 1190 166 1024 .785 1371 1205 1.273 .924 -.349 -.115
8 823 1091 128 230 695 861 829 1125 133 237 701 895 0 0 576 676 40 87 76 83 71 75 1556 1596 .807 1.239 1.277 2.108 1.27 3.073 120 387 1.125 .93 120 2180 18620 69 81 177 189 0 797 168 629 .905 822 654 1.104 .933 -.143 -.1
9 20017 15749 138 240 19879 15509 16504 13151 146 245 16366 12911 0 0 16730 13608 46 85 92 93 88 87 35388 29277 1.282 .78 .789 1.775 .796 4.718 156 649 .778 .98 150 2340 18610 66 81 191 206 0 11511 175 11335 .57 9612 9437 1.754 .577 -.81 -.794
10 1146 1282 149 244 997 1038 1328 1474 153 252 1179 1230 0 0 621 726 46 84 93 88 90 80 2035 2409 .961 1.041 1.043 1.803 1.037 5.293 120 374 1.015 .93 120 2510 18620 69 81 210 222 0 937 178 759 .761 1077 899 1.314 .763 -.394 -.391
11 5308 4367 136 240 5172 4127 4828 2699 143 246 4692 2459 0 0 5734 4731 44 86 89 82 82 77 9299 7151 1.253 .798 .524 1.279 .824 2.054 208 728 .774 .95 160 2680 18620 67 83 225 241 0 3192 175 3016 .583 1973 1797 1.715 .383 -.778 -1.384
12 630 1096 134 225 496 871 682 1267 140 235 548 1042 0 0 345 618 46 87 87 85 83 78 1367 1590 .569 1.756 1.901 1.911 1.733 1.215 120 422 1.633 .93 120 2840 18610 68 80 243 255 0 801 164 637 1.283 926 762 .779 1.39 .36 .475
13 2772 2317 125 230 2647 2087 2114 1708 130 238 1989 1478 0 0 2320 1904 40 88 92 88 92 86 4734 3467 1.268 .788 .743 1.313 .766 1.855 80 400 .773 .96 110 2990 18630 70 81 258 269 0 1693 168 1525 .576 1248 1080 1.735 .543 -.795 -.881
14 507 837 128 236 379 601 536 856 134 244 408 620 0 0 262 432 48 94 85 82 77 78 980 1028 .631 1.586 1.52 2.022 1.604 2.132 80 417 1.445 .88 110 3160 18620 69 80 275 286 0 612 172 439 1.159 626 453 .863 1.111 .213 .151
15 398 671 127 225 271 446 298 466 133 237 171 241 0 0 283 482 47 93 68 61 57 55 717 412 .608 1.646 1.409 2.072 1.574 2.077 120 495 1.485 .88 120 3310 18610 68 80 290 302 0 490 164 326 1.203 341 176 .831 1.03 .266 .043
16 769 1185 128 226 641 959 830 1261 135 237 702 1035 0 0 413 581 45 88 91 96 85 86 1600 1737 .668 1.496 1.474 2.865 1.478 5.941 80 382 1.369 .93 110 3480 18620 69 80 307 318 0 866 165 701 1.093 922 756 .915 1.078 .129 .108
17 3670 2605 130 227 3540 2378 1435 1456 135 235 1305 1229 0 0 3787 2537 45 83 73 72 68 67 5918 2534 1.489 .672 .942 1.851 .715 3.35 120 457 .648 .97 120 3630 18620 69 81 322 334 0 1904 166 1738 .491 1064 898 2.037 .688 -1.026 -.539
18 725 1195 130 227 595 968 747 1194 135 238 617 967 0 0 390 658 42 85 88 91 87 87 1563 1584 .615 1.627 1.567 2.942 1.538 6.071 80 396 1.538 .93 110 3800 18610 68 79 339 350 0 873 166 708 1.189 873 707 .841 1.145 .25 .196
19 927 1212 126 235 801 977 633 859 132 245 507 624 0 0 852 1041 39 90 71 75 63 68 1778 1131 .82 1.22 1.231 2.575 1.227 4.155 120 431 1.161 .95 120 3950 18610 68 80 354 366 0 886 172 714 .891 628 456 1.122 .9 -.166 -.153
20 3185 2714 121 229 3064 2485 2892 1894 126 237 2771 1665 0 0 2395 2289 36 85 87 83 82 80 5549 4436 1.233 .811 .601 1.748 .818 6.625 156 542 .848 .96 140 4110 18630 69 83 369 383 0 1984 167 1816 .593 1384 1217 1.687 .439 -.754 -1.187

Total number of rows: 21504

Table truncated, full table size 4821 Kbytes.




Supplementary data files not provided
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