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Sample GSM94432 Query DataSets for GSM94432
Status Public on Feb 01, 2006
Title "MA41-3 (A) (no selection) (red, channel 2) vs. MA24-3 (B) (no selection) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA24-3 (B) (no selection) (green)
Organism Caenorhabditis elegans
Characteristics MA24-3 (B) (no selection) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA41-3 (A) (no selection) (red)
Organism Caenorhabditis elegans
Characteristics MA41-3 (A) (no selection) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12939.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 2103 3125 107 227 1996 2898 1933 2974 159 256 1826 2747 0 0 1642 2243 670 385 67 83 56 75 4894 4573 .689 1.452 1.504 1.872 1.552 1.8 120 569 1.309 .92 130 1680 16430 84 97 97 110 0 1692 123 1569 .786 1611 1488 1.272 .815 -.347 -.296
2 2766 3781 100 233 2666 3548 1299 2796 119 240 1199 2563 1 0 9919 8595 74 68 83 90 79 87 6214 3762 .751 1.331 2.138 2.559 2.129 2.196 120 464 .938 .96 130 1850 16420 83 96 114 127 0 2048 126 1921 .721 1514 1388 1.387 1.158 -.472 .211
3 1169 2634 98 262 1071 2372 976 2532 109 285 878 2270 0 0 1030 1989 72 122 75 83 67 75 3443 3148 .452 2.215 2.585 4.232 2.324 9.394 120 395 1.93 .94 120 2010 16420 84 96 131 143 0 1426 142 1285 1.199 1371 1229 .834 1.4 .262 .486
4 1787 2698 98 280 1689 2418 2119 3166 108 297 2021 2886 0 0 1149 1673 67 114 85 90 84 86 4107 4907 .699 1.432 1.428 2.055 1.469 2.295 120 453 1.374 .96 130 2180 16430 84 97 147 160 0 1461 152 1310 .775 1715 1563 1.29 .773 -.367 -.371
5 5230 5779 100 259 5130 5520 3650 4518 108 264 3550 4259 0 0 5080 5397 56 72 74 80 66 72 10650 7809 .929 1.076 1.2 2.453 1.204 3.342 120 420 1.014 .95 120 2360 16420 84 96 166 178 0 3130 140 2989 .583 2447 2307 1.716 .65 -.779 -.622
6 445 767 100 255 345 512 171 497 110 262 71 242 0 0 688 775 59 73 53 69 30 61 857 313 .674 1.484 3.408 4.153 2.201 6.453 120 407 1.089 .92 120 2500 16420 84 96 180 192 0 415 138 277 .804 269 131 1.244 1.846 -.315 .884
7 1475 2391 99 256 1376 2135 1612 2736 107 260 1513 2480 0 0 1019 1453 39 59 89 95 85 87 3511 3993 .644 1.552 1.639 2.786 1.576 5.491 120 417 1.401 .93 120 2660 16410 83 95 196 208 0 1295 139 1156 .84 1482 1343 1.19 .888 -.251 -.172
8 1326 1629 106 263 1220 1366 1105 1543 114 272 999 1280 0 0 1206 1193 44 68 80 86 72 78 2586 2279 .893 1.12 1.281 3.769 1.247 9.179 120 406 .957 .92 120 2820 16410 83 95 212 224 0 882 142 740 .606 836 693 1.649 .694 -.722 -.527
9 17828 11854 111 271 17717 11583 24528 14322 119 287 24417 14051 0 0 12480 8418 44 88 94 95 88 90 29300 38468 1.53 .654 .575 1.462 .711 2.308 120 436 .639 .96 130 3000 16410 82 95 229 242 0 6420 147 6273 .354 7756 7610 2.824 .312 -1.498 -1.682
10 1541 3080 111 273 1430 2807 1396 3176 117 282 1285 2903 0 0 1313 2399 42 70 81 88 75 83 4237 4188 .509 1.963 2.259 4.014 2.12 8.969 120 370 1.809 .96 120 3160 16400 82 94 246 258 0 1668 148 1520 1.063 1720 1572 .941 1.223 .088 .291
11 3805 3594 111 273 3694 3321 4561 4391 117 274 4450 4118 0 0 2403 2314 40 59 93 91 89 89 7015 8568 1.112 .899 .925 1.329 .979 1.993 120 432 .875 .95 130 3320 16410 82 95 261 274 0 1946 148 1799 .487 2378 2230 2.054 .501 -1.038 -.997
12 1092 2108 111 277 981 1831 957 1919 117 278 846 1642 0 0 881 1612 37 64 83 83 75 77 2812 2488 .536 1.866 1.941 3.705 1.932 9.061 120 403 1.776 .96 120 3490 16400 82 94 279 291 0 1142 150 992 1.011 1039 889 .989 1.051 .016 .072
13 3369 3773 112 282 3257 3491 2282 2845 128 287 2170 2563 0 0 3259 3549 187 71 64 84 62 73 6748 4733 .933 1.072 1.181 2.166 1.226 4.175 120 418 1.04 .96 120 3640 16400 82 94 294 306 0 2043 153 1891 .58 1541 1388 1.723 .64 -.785 -.645
14 735 1628 110 285 625 1343 747 1705 127 288 637 1420 0 0 550 1063 182 62 65 85 60 78 1968 2057 .465 2.149 2.229 3.079 2.334 4.116 120 441 1.826 .9 120 3810 16390 81 93 311 323 0 882 154 727 1.164 923 769 .859 1.207 .219 .272
15 893 1824 107 286 786 1538 761 1858 112 292 654 1572 0 0 692 1251 36 73 82 88 77 78 2324 2226 .511 1.957 2.404 3.228 2.096 7.447 120 429 1.736 .92 120 3960 16390 81 93 326 338 0 988 155 833 1.06 1006 851 .944 1.302 .084 .38
16 1170 2254 107 284 1063 1970 1138 2538 113 288 1031 2254 0 0 884 1517 39 60 85 90 78 83 3033 3285 .54 1.853 2.186 2.383 1.948 2.209 120 408 1.707 .95 120 4130 16390 81 93 343 355 0 1221 154 1067 1.004 1374 1221 .996 1.184 .005 .244
17 4069 4356 108 294 3961 4062 3208 2885 119 305 3100 2591 0 0 3911 4084 65 82 75 78 66 75 8023 5691 .975 1.025 .836 1.849 1.067 2.678 120 379 .998 .96 120 4290 16390 81 93 359 371 0 2359 159 2200 .555 1562 1403 1.801 .453 -.848 -1.144
18 1474 2857 111 302 1363 2555 1413 2839 120 316 1302 2537 0 0 1122 2054 63 86 83 90 80 81 3918 3839 .533 1.875 1.949 2.787 1.878 3.638 120 409 1.78 .96 120 4450 16380 80 92 375 387 0 1547 164 1384 1.015 1538 1374 .985 1.055 .022 .078
19 1804 2699 108 297 1696 2402 1764 2938 114 308 1656 2641 0 0 1423 1949 37 77 83 81 78 75 4098 4297 .706 1.416 1.595 2.637 1.446 5.352 120 369 1.335 .96 120 4620 16390 81 93 392 404 0 1462 161 1301 .767 1591 1430 1.304 .864 -.383 -.211
20 4923 4785 108 311 4815 4474 6595 5326 119 318 6487 5015 0 0 3382 3453 50 80 87 89 84 85 9289 11502 1.076 .929 .773 1.664 .957 3.078 120 441 .939 .97 130 4770 16390 80 93 406 419 0 2591 168 2423 .503 2884 2716 1.987 .419 -.991 -1.256

Total number of rows: 21504

Table truncated, full table size 4926 Kbytes.




Supplementary data files not provided
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