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Sample GSM94465 Query DataSets for GSM94465
Status Public on Feb 01, 2006
Title "MA83-3(A) (red, channel 2) vs. MA41-3(B) (green, channel 1)"
Sample type RNA
 
Channel 1
Source name MA41-3(B) (green)
Organism Caenorhabditis elegans
Characteristics MA41-3(B) (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name MA83-3(A) (red)
Organism Caenorhabditis elegans
Characteristics MA83-3(A) (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16497.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 2515 3251 225 414 2290 2837 1255 1807 228 421 1030 1393 0 0 2453 2898 69 114 77 81 70 73 5127 2423 .807 1.239 1.352 1.442 1.312 2.587 120 632 1.217 .95 130 1040 18580 64 77 62 75 0 2046 261 1786 .78 1137 877 1.282 .851 -.359 -.232
2 1238 1959 214 378 1024 1581 1038 1669 217 382 824 1291 0 0 966 1448 64 101 80 85 75 75 2605 2115 .648 1.544 1.567 1.574 1.502 2.224 120 437 1.554 .95 130 1200 18590 65 78 78 91 0 1233 238 995 .972 1051 813 1.029 .986 -.041 -.02
3 651 1031 213 367 438 664 333 645 219 370 120 278 0 0 654 894 64 92 62 67 48 55 1102 398 .66 1.516 2.317 1.882 1.681 2.702 120 407 1.454 .91 120 1370 18590 66 78 96 108 0 649 231 418 .954 406 175 1.048 1.458 -.068 .544
4 1335 1963 217 363 1118 1600 467 971 221 367 250 608 0 0 1321 1817 67 92 65 67 58 62 2718 858 .699 1.431 2.432 1.383 1.389 2.706 120 410 1.423 .95 120 1530 18590 66 78 112 124 0 1236 228 1007 .901 611 383 1.11 1.531 -.151 .614
5 4990 3266 212 353 4778 2913 2063 2390 221 363 1851 2037 0 0 4970 2970 72 95 77 78 69 67 7691 3888 1.64 .61 1.1 .757 .659 3.565 120 465 .591 .96 120 1690 18590 66 78 128 140 0 2056 222 1834 .384 1504 1282 2.606 .693 -1.382 -.53
6 615 815 204 317 411 498 366 632 215 328 162 315 0 0 540 486 71 85 63 88 51 71 909 477 .825 1.212 1.944 1.674 1.459 2.692 52 262 1.032 .89 90 1850 18580 66 75 145 154 0 513 200 313 .763 398 198 1.311 1.224 -.391 .292
7 1280 1778 201 339 1079 1439 1234 1702 211 342 1033 1363 0 0 848 1131 74 89 85 88 81 83 2518 2396 .75 1.334 1.319 1.417 1.379 2.014 156 564 1.362 .94 140 2000 18580 64 78 158 172 0 1119 213 906 .839 1071 858 1.191 .831 -.252 -.268
8 1308 1648 197 341 1111 1307 1141 1608 206 342 944 1267 0 0 921 1038 68 87 86 90 77 83 2418 2211 .85 1.176 1.342 1.332 1.196 2.177 120 425 1.165 .94 130 2170 18580 64 77 175 188 0 1037 215 823 .741 1012 798 1.35 .845 -.433 -.243
9 9176 12815 195 332 8981 12483 8485 10907 207 337 8290 10575 0 0 7669 10726 69 93 87 89 82 85 21464 18865 .719 1.39 1.276 1.525 1.408 2.473 156 566 1.408 .97 150 2340 18580 63 78 191 206 0 8067 209 7858 .875 6866 6657 1.143 .803 -.193 -.317
10 1263 1880 192 319 1071 1561 1358 1720 203 326 1166 1401 0 0 760 1155 69 95 91 91 87 86 2632 2567 .686 1.458 1.202 1.382 1.457 1.86 120 399 1.538 .93 130 2500 18570 63 76 208 221 0 1183 201 983 .917 1083 882 1.09 .756 -.124 -.403
11 2746 3579 189 319 2557 3260 2689 3625 198 323 2500 3306 0 0 1777 2445 68 89 91 92 87 85 5817 5806 .784 1.275 1.322 1.235 1.268 2.211 156 579 1.342 .95 150 2650 18580 63 78 222 237 0 2253 201 2052 .803 2282 2081 1.246 .832 -.317 -.265
12 954 1701 185 315 769 1386 1024 1836 193 320 839 1521 0 0 616 1040 66 89 84 85 75 79 2155 2360 .555 1.802 1.813 1.817 1.727 2.166 120 474 1.821 .94 130 2830 18570 63 76 241 254 0 1071 198 872 1.135 1156 957 .881 1.141 .182 .19
13 2165 2989 187 309 1978 2680 1475 2092 196 316 1288 1783 0 0 1881 2516 66 86 82 87 77 81 4658 3071 .738 1.355 1.384 1.388 1.381 2.265 80 369 1.368 .95 110 2970 18580 65 76 256 267 0 1881 195 1687 .853 1317 1122 1.173 .871 -.23 -.199
14 861 1422 192 319 669 1103 762 1221 200 323 570 902 0 0 555 901 64 86 85 86 77 77 1772 1472 .607 1.649 1.582 1.612 1.564 2.276 80 410 1.714 .92 110 3140 18580 65 76 273 284 0 895 201 694 1.038 769 568 .964 .996 .054 -.006
15 606 1078 187 322 419 756 377 688 198 328 190 366 0 0 506 914 86 91 60 61 50 56 1175 556 .554 1.804 1.926 1.64 1.927 2.613 120 442 1.898 .92 120 3300 18570 64 76 289 301 0 679 203 476 1.136 433 230 .88 1.213 .184 .278
16 930 1583 182 325 748 1258 739 1240 195 334 557 915 0 0 756 1295 87 91 64 73 58 67 2006 1472 .595 1.682 1.643 1.789 1.811 2.497 120 394 1.765 .94 120 3460 18570 64 76 305 317 0 996 205 792 1.059 781 576 .945 1.034 .082 .048
17 3005 3100 182 353 2823 2747 1224 1479 190 356 1042 1126 0 0 3139 3153 59 92 73 68 65 64 5570 2168 1.028 .973 1.081 .907 1.031 2.91 120 389 .997 .95 120 3620 18580 65 77 321 333 0 1951 222 1729 .613 931 709 1.633 .68 -.707 -.556
18 1275 1965 178 357 1097 1608 1287 2067 189 362 1109 1710 0 0 787 1107 63 89 83 92 82 87 2705 2819 .682 1.466 1.542 1.561 1.484 1.9 80 379 1.495 .94 110 3780 18570 64 75 337 348 0 1237 225 1012 .923 1301 1076 1.084 .971 -.116 -.043
19 1335 2372 182 337 1153 2035 1298 2194 193 344 1116 1857 0 0 820 1443 132 90 86 93 76 92 3188 2973 .567 1.765 1.664 1.811 1.822 2.117 80 388 1.828 .95 110 3930 18570 64 75 352 363 0 1493 212 1281 1.111 1381 1169 .9 1.047 .152 .067
20 1799 2724 171 342 1628 2382 1824 2531 181 354 1653 2189 0 0 1193 1995 108 106 83 84 80 80 4010 3842 .683 1.463 1.324 1.255 1.489 2.024 156 643 1.599 .95 150 4100 18580 63 78 367 382 0 1715 215 1499 .921 1593 1378 1.086 .834 -.119 -.263

Total number of rows: 21504

Table truncated, full table size 4851 Kbytes.




Supplementary data files not provided
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