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Sample GSM90827 Query DataSets for GSM90827
Status Public on Jan 06, 2006
Title 26C Control, t=336hr
Sample type RNA
 
Channel 1
Source name Liver Reference RNA 4/17/02 (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics Liver Reference RNA 4/17/02 (pooled, 1 ug poly-A)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CO-336, adult liver (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics CO-336, adult liver (pooled, 1 ug poly-A)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: temperature acclimation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/32693.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 05, 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 GPL3311
Series (1)
GSE3981 Temperature acclimation

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
LOG_RAT2N_MEAN 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
VALUE 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 LOG_RAT2N_MEAN VALUE
1 32290 34404 143 58 32147 34346 32255 33499 191 77 32112 33441 0 0 8692 9764 250 86 100 100 100 100 66493 65553 .936 1.068 1.041 1 1 1 156 995 1 1 140 2020 25880 68 82 78 92 0 38656 65 38591 1.2 37639 37574 .833 1.17 .264 .227
2 11595 8532 140 58 11455 8474 12414 8981 150 64 12274 8923 0 0 2687 2006 58 32 100 100 100 100 19929 21197 1.352 .74 .727 1 1 1 156 953 1 .99 140 2260 25880 68 82 102 116 0 9587 65 9521 .831 10091 10026 1.203 .817 -.267 -.292
3 13383 10474 132 55 13251 10419 14051 11112 132 57 13919 11057 0 0 3579 3084 16 12 100 100 100 100 23670 24976 1.272 .786 .794 1 1 1 156 968 1 1 140 2510 25880 68 82 127 141 0 11769 62 11707 .883 12485 12424 1.132 .893 -.179 -.164
4 1422 1135 127 54 1295 1081 1449 1157 127 55 1322 1103 0 0 324 280 15 11 100 100 100 100 2376 2425 1.198 .835 .834 1 1 1 156 952 1 .99 140 2750 25880 68 82 151 165 0 1275 61 1215 .938 1300 1239 1.066 .937 -.092 -.093
5 1946 1480 124 52 1822 1428 2058 1558 125 54 1934 1506 0 0 355 301 17 12 100 100 100 100 3250 3440 1.276 .784 .779 1 1 1 156 937 1 .99 140 3000 25880 68 82 176 190 0 1663 58 1604 .881 1751 1692 1.136 .875 -.183 -.193
6 5887 4606 120 50 5767 4556 6295 4894 122 51 6175 4844 0 0 1620 1123 19 11 100 100 99 100 10323 11019 1.266 .79 .784 1 1 1 156 927 1 .99 140 3230 25870 67 81 199 213 0 5175 56 5119 .888 5499 5443 1.127 .881 -.172 -.182
7 15252 12436 121 50 15131 12386 17198 13859 123 51 17077 13809 0 0 4793 3578 16 11 100 100 99 100 27517 30886 1.222 .819 .809 1 1 1 156 943 1 .99 140 3470 25870 67 81 223 237 0 13973 56 13917 .92 15572 15516 1.087 .909 -.121 -.138
8 1128 798 123 50 1005 748 1185 825 141 52 1062 775 0 0 316 228 499 25 92 100 52 100 1753 1837 1.344 .744 .73 1 1 1 156 937 1 .99 140 3710 25880 68 82 247 261 0 897 56 840 .836 927 871 1.196 .82 -.258 -.286
9 445 188 122 50 323 138 438 179 178 54 316 129 0 0 99 58 839 47 0 97 0 80 461 445 2.341 .427 .408 1 1 1 156 904 1 .48 140 3950 25880 68 82 271 285 0 211 56 155 .48 201 145 2.083 .459 -1.059 -1.124
10 5050 3730 124 50 4926 3680 5292 3862 133 56 5168 3812 0 0 2198 1601 106 64 100 100 100 100 8606 8980 1.339 .747 .738 1 1 1 156 1020 1 .99 150 4170 25880 67 82 292 307 0 4191 56 4135 .839 4339 4283 1.191 .829 -.253 -.271
11 1804 1317 123 51 1681 1266 1934 1422 133 57 1811 1371 0 0 408 323 108 66 99 99 99 99 2947 3182 1.328 .753 .757 1 1 1 156 966 1 .99 140 4430 25880 68 82 319 333 0 1480 57 1422 .846 1598 1540 1.182 .851 -.241 -.233
12 999 622 121 52 878 570 1042 650 124 53 921 598 0 0 192 138 32 11 100 100 100 100 1448 1519 1.54 .649 .649 1 1 1 156 937 1 .98 140 4670 25880 68 82 343 357 0 699 58 640 .729 730 672 1.371 .73 -.455 -.455
13 1886 1238 122 52 1764 1186 2008 1349 129 53 1886 1297 0 0 510 322 40 12 100 100 99 100 2950 3183 1.487 .672 .688 1 1 1 156 985 1 .99 140 4910 25870 67 81 367 381 0 1391 58 1333 .755 1516 1457 1.324 .773 -.405 -.372
14 2452 1425 120 51 2332 1374 2500 1437 126 53 2380 1386 0 0 286 138 51 23 100 100 100 100 3706 3766 1.697 .589 .582 1 1 1 120 828 1 .99 130 5150 25870 67 80 391 404 0 1601 57 1544 .662 1615 1557 1.511 .654 -.595 -.612
15 1403 900 116 50 1287 850 1462 930 125 55 1346 880 0 0 231 157 102 53 100 100 100 100 2137 2226 1.514 .66 .654 1 1 1 156 952 1 .99 140 5390 25880 68 82 415 429 0 1011 56 955 .742 1045 989 1.348 .735 -.43 -.445
16 1389 1150 118 49 1271 1101 1442 1200 120 50 1324 1151 0 0 314 254 23 11 100 100 100 100 2372 2475 1.154 .866 .869 1 1 1 156 937 1 .99 140 5630 25880 68 82 439 453 0 1292 55 1237 .973 1348 1293 1.027 .977 -.039 -.034
17 3651 2062 118 49 3533 2013 3860 2174 120 51 3742 2125 0 0 664 364 21 10 100 100 100 100 5546 5867 1.755 .57 .568 1 1 1 156 1044 1 .99 150 5870 25870 66 81 462 477 0 2317 55 2262 .64 2443 2388 1.562 .638 -.643 -.648
18 9155 6857 120 51 9035 6806 9614 7207 121 51 9494 7156 0 0 1416 1092 14 12 100 100 100 100 15841 16650 1.328 .753 .754 1 1 1 156 1005 1 .99 140 6110 25880 68 82 487 501 0 7704 57 7647 .846 8098 8040 1.181 .847 -.241 -.24
19 27945 31739 139 56 27806 31683 27781 32408 155 62 27642 32352 0 0 7395 8987 99 27 100 100 100 100 59489 59994 .878 1.139 1.17 1 1 1 156 953 1 1 140 2030 26120 92 106 79 93 0 35662 63 35599 1.28 36413 36351 .781 1.315 .356 .395
20 40574 44515 139 59 40435 44456 43164 47279 142 61 43025 47220 0 0 9420 11266 31 16 100 100 100 100 84891 90245 .91 1.099 1.098 1 1 1 156 885 1 .99 140 2270 26120 92 106 103 117 0 50017 66 49951 1.235 53122 53056 .81 1.233 .305 .302

Total number of rows: 4992

Table truncated, full table size 1106 Kbytes.




Supplementary data files not provided
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