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Sample GSM94431 Query DataSets for GSM94431
Status Public on Feb 01, 2006
Title "MA41-4 (A) (no selection) (red, channel 2) vs. MA24-4 (B) (no selection) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA24-4 (B) (green)
Organism Caenorhabditis elegans
Characteristics MA24-4 (B) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA41-4 (A) (red)
Organism Caenorhabditis elegans
Characteristics MA41-4 (A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12938.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 1486 1908 96 244 1390 1664 1495 1850 100 250 1399 1606 0 0 1057 1326 33 58 86 81 81 80 3054 3005 .835 1.197 1.148 1.58 1.224 1.97 120 633 1.183 .97 130 2480 16230 64 77 93 106 0 1022 131 892 .642 991 861 1.559 .615 -.64 -.701
2 788 1262 96 252 692 1010 743 1415 101 255 647 1163 0 0 537 727 29 48 82 85 80 80 1702 1810 .685 1.46 1.798 1.972 1.474 1.963 120 448 1.337 .94 120 2640 16220 64 76 110 122 0 676 135 541 .782 758 623 1.279 .963 -.354 -.054
3 1205 1955 98 258 1107 1697 1175 2121 101 262 1077 1863 0 0 747 945 27 52 92 93 87 93 2804 2940 .652 1.533 1.73 3.042 1.649 8.355 80 352 1.346 .94 100 2800 16230 66 76 127 137 0 1048 138 909 .821 1137 998 1.217 .927 -.284 -.109
4 1829 1861 98 256 1731 1605 1971 2024 101 260 1873 1768 0 0 748 767 25 49 100 97 100 96 3336 3641 1.079 .927 .944 .979 .945 .761 80 407 .905 .96 110 2960 16240 66 77 142 153 0 997 137 860 .497 1085 947 2.013 .506 -1.009 -.983
5 3877 4338 100 268 3777 4070 2795 3902 102 272 2695 3634 0 0 3619 3770 27 52 78 84 74 78 7847 6329 .928 1.078 1.348 2.892 1.126 5.214 120 498 1.014 .96 120 3140 16240 66 78 160 172 0 2325 144 2181 .577 2091 1947 1.732 .723 -.792 -.469
6 318 713 100 272 218 441 160 568 103 276 60 296 0 0 427 495 26 53 76 88 56 81 659 356 .494 2.023 4.933 6.069 4.026 7.361 80 377 1.152 .86 110 3300 16240 66 77 176 187 0 382 146 236 1.084 304 159 .922 2.644 .116 1.403
7 1066 1468 101 272 965 1196 1043 1580 104 278 942 1308 0 0 700 883 25 59 92 85 86 80 2161 2250 .807 1.239 1.389 1.517 1.284 1.271 120 473 1.159 .92 120 3450 16240 66 78 191 203 0 787 146 641 .664 847 701 1.506 .744 -.59 -.426
8 933 1253 107 281 826 972 739 1157 110 287 632 876 0 0 761 745 27 57 92 93 86 88 1798 1508 .85 1.177 1.386 1.957 1.183 2.39 80 410 1.005 .93 110 3620 16240 66 77 208 219 0 671 151 521 .631 620 469 1.586 .743 -.665 -.429
9 18359 8830 108 317 18251 8513 22803 10399 112 317 22695 10082 0 0 13796 6583 28 57 95 92 91 90 26764 32777 2.144 .466 .444 1.632 .478 4.916 120 474 .454 .96 130 3790 16250 66 79 224 237 0 4732 170 4562 .25 5573 5403 4.001 .238 -2 -2.071
10 1886 3071 110 326 1776 2745 1920 3349 115 326 1810 3023 0 0 1079 1306 47 55 95 100 92 100 4521 4833 .647 1.546 1.67 3.691 1.633 10.372 80 332 1.335 .92 110 3940 16250 67 78 240 251 0 1646 175 1471 .828 1795 1620 1.207 .895 -.272 -.16
11 3300 2482 110 333 3190 2149 3903 2890 115 336 3793 2557 0 0 2256 1652 42 60 88 90 80 85 5339 6350 1.484 .674 .674 1.625 .736 3.62 120 440 .657 .94 130 4100 16260 67 80 255 268 0 1330 178 1152 .361 1549 1370 2.77 .361 -1.47 -1.469
12 885 1568 110 342 775 1226 763 1608 115 345 653 1266 0 0 734 1077 34 66 85 80 75 74 2001 1919 .632 1.582 1.939 2.649 1.605 3.617 120 441 1.369 .9 120 4260 16250 67 79 272 284 0 840 183 657 .848 862 678 1.18 1.039 -.238 .055
13 3649 3273 111 346 3538 2927 3941 3722 116 349 3830 3376 0 0 2064 1711 31 64 100 98 100 95 6465 7206 1.209 .827 .881 1.232 .864 1.762 80 360 .788 .95 110 4420 16260 68 79 288 299 0 1754 185 1569 .443 1995 1809 2.256 .472 -1.174 -1.082
14 472 923 113 353 359 570 379 964 115 359 266 611 0 0 358 515 28 65 73 70 65 65 929 877 .63 1.588 2.297 3.174 1.665 5.153 120 444 1.317 .87 120 4580 16260 68 80 304 316 0 495 189 305 .851 517 327 1.175 1.231 -.233 .3
15 649 1282 113 345 536 937 539 1267 116 354 426 922 0 0 566 896 30 64 75 75 66 67 1473 1348 .572 1.748 2.164 3.79 1.788 8.635 120 432 1.475 .9 120 4740 16260 68 80 320 332 0 687 185 502 .937 679 494 1.067 1.16 -.094 .214
16 890 1633 114 350 776 1283 852 1739 116 351 738 1389 0 0 700 1062 31 61 86 85 79 75 2059 2127 .605 1.653 1.882 2.344 1.559 2.5 120 444 1.475 .93 120 4910 16260 68 80 337 349 0 875 188 688 .886 932 744 1.129 1.009 -.175 .012
17 4694 4434 117 356 4577 4078 5356 5139 119 354 5239 4783 0 0 2816 2540 29 57 96 97 92 95 8655 10022 1.122 .891 .913 2.298 .893 6.36 80 381 .853 .95 110 5070 16260 68 79 353 364 0 2376 191 2185 .477 2754 2563 2.094 .489 -1.067 -1.031
18 1556 2684 115 360 1441 2324 1654 2969 119 357 1539 2609 0 0 740 1224 27 59 98 97 96 95 3765 4148 .62 1.613 1.695 2.156 1.631 3.318 80 390 1.567 .96 110 5230 16260 68 79 369 380 0 1438 193 1245 .864 1591 1398 1.157 .908 -.21 -.139
19 1254 1761 114 364 1140 1397 1366 1996 119 364 1252 1632 0 0 945 1139 29 60 85 89 81 79 2537 2884 .816 1.225 1.304 1.766 1.359 1.878 120 396 1.126 .92 120 5390 16270 69 81 385 397 0 944 195 749 .657 1070 875 1.523 .699 -.607 -.518
20 3662 2832 120 363 3542 2469 4639 3475 124 365 4519 3112 0 0 2537 1893 30 62 89 91 85 83 6011 7631 1.435 .697 .689 1.103 .715 2.217 120 384 .684 .95 120 5540 16270 69 81 400 412 0 1518 195 1323 .374 1862 1668 2.677 .369 -1.421 -1.438

Total number of rows: 21504

Table truncated, full table size 4903 Kbytes.




Supplementary data files not provided
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