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Sample GSM90831 Query DataSets for GSM90831
Status Public on Jan 06, 2006
Title Cycle, t=108hr
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 CY-108, adult liver (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics CY-108, adult liver (pooled, 1 ug poly-A)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: temperature acclimation, cycling acclimation
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/31119.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 32314 49970 87 59 32227 49911 33229 51208 111 94 33142 51149 0 0 5671 9500 265 362 100 100 100 100 82138 84291 .646 1.549 1.543 1 1 1 120 876 1 1 130 2090 25780 123 136 112 125 0 46701 55 46646 1.447 47858 47803 .691 1.442 .533 .528
2 16536 27366 90 62 16446 27304 16690 27535 151 146 16600 27473 0 0 1123 1449 581 777 100 100 100 100 43750 44073 .602 1.66 1.655 1 1 1 120 860 1 1 130 2330 25780 123 136 136 149 0 25576 58 25518 1.552 25734 25676 .644 1.547 .634 .629
3 20436 23410 87 59 20349 23351 21739 25058 119 102 21652 24999 0 0 3107 3644 454 626 100 100 100 100 43700 46651 .871 1.148 1.155 1 1 1 120 848 1 1 130 2580 25780 123 136 161 174 0 21879 55 21823 1.072 23419 23364 .932 1.079 .101 .11
4 1654 2040 80 54 1574 1986 1682 2090 87 60 1602 2036 0 0 516 581 47 62 98 100 96 99 3560 3638 .793 1.262 1.271 1 1 1 156 955 1 .99 140 2820 25780 123 137 185 199 0 1907 50 1856 1.179 1953 1903 .848 1.188 .238 .248
5 2908 3029 78 51 2830 2978 3033 3140 82 55 2955 3089 0 0 470 465 29 29 100 100 100 100 5808 6044 .95 1.052 1.045 1 1 1 156 923 1 .99 140 3060 25780 123 137 209 223 0 2831 48 2783 .983 2935 2887 1.017 .977 -.024 -.034
6 8821 11187 79 50 8742 11137 9576 11923 82 55 9497 11873 0 0 2087 2596 25 39 100 100 100 100 19879 21370 .785 1.274 1.25 1 1 1 156 936 1 .99 140 3290 25780 123 137 232 246 0 10455 47 10408 1.191 11143 11096 .84 1.168 .252 .225
7 19433 21896 80 52 19353 21844 20749 23369 84 56 20669 23317 0 0 3997 4557 31 40 100 100 100 100 41197 43986 .886 1.129 1.128 1 1 1 156 941 1 .99 140 3540 25780 123 137 257 271 0 20464 49 20415 1.055 21840 21792 .948 1.054 .077 .076
8 2008 2381 79 52 1929 2329 1975 2317 90 63 1896 2265 0 0 486 514 112 110 100 100 100 100 4258 4161 .828 1.207 1.195 1 1 1 120 799 1 .99 130 3760 25770 122 135 279 292 0 2225 49 2177 1.128 2165 2117 .886 1.116 .174 .159
9 611 836 80 52 531 784 596 820 89 63 516 768 0 0 155 208 108 103 100 100 97 100 1315 1284 .677 1.476 1.488 1 1 1 156 951 1 .96 140 4010 25780 123 137 304 318 0 781 49 733 1.38 766 718 .725 1.391 .465 .476
10 8644 10771 82 55 8562 10716 8668 10716 85 57 8586 10661 0 0 2401 3255 22 23 100 100 100 100 19278 19247 .799 1.252 1.242 1 1 1 156 937 1 .99 140 4250 25780 123 137 328 342 0 10066 51 10015 1.17 10015 9964 .855 1.16 .226 .215
11 2859 3570 84 58 2775 3512 2885 3589 87 61 2801 3531 0 0 293 313 30 35 100 100 100 100 6287 6332 .79 1.266 1.261 1 1 1 120 826 1 .99 130 4490 25770 122 135 352 365 0 3336 54 3282 1.183 3354 3300 .845 1.178 .242 .237
12 1814 2234 88 60 1726 2174 1772 2175 104 78 1684 2115 0 0 418 391 127 156 100 100 100 100 3900 3799 .794 1.26 1.256 1 1 1 120 838 1 .98 130 4720 25770 122 135 375 388 0 2088 56 2032 1.177 2033 1977 .85 1.174 .235 .231
13 2998 3176 81 55 2917 3121 3019 3155 97 70 2938 3100 0 0 342 362 124 122 100 100 100 100 6038 6038 .935 1.07 1.055 1 1 1 120 862 1 .99 130 4960 25770 122 135 399 412 0 2968 51 2917 1 2949 2897 1 .986 0 -.02
14 3548 4570 81 52 3467 4518 3707 4792 89 60 3626 4740 0 0 532 742 88 78 100 100 100 100 7985 8366 .767 1.303 1.307 1 1 1 156 957 1 .99 140 5210 25770 122 136 424 438 0 4271 49 4222 1.218 4479 4430 .821 1.222 .284 .289
15 1946 2168 82 52 1864 2116 2015 2219 84 54 1933 2167 0 0 344 315 19 25 100 100 100 100 3980 4100 .881 1.135 1.121 1 1 1 156 927 1 .99 140 5450 25770 122 136 448 462 0 2026 49 1978 1.061 2074 2025 .943 1.048 .085 .067
16 2227 2134 82 52 2145 2082 2258 2112 84 54 2176 2060 0 0 463 482 11 14 100 100 100 100 4227 4236 1.03 .971 .947 1 1 1 156 927 1 .99 140 5690 25770 122 136 472 486 0 1994 49 1946 .907 1974 1925 1.102 .885 -.141 -.177
17 5879 6256 82 52 5797 6204 6137 6492 85 57 6055 6440 0 0 902 1182 32 87 100 100 100 100 12001 12495 .934 1.07 1.064 1 1 1 156 929 1 .99 140 5930 25770 122 136 496 510 0 5847 49 5798 1 6067 6019 1 .994 0 -.009
18 12731 12089 83 55 12648 12034 12633 11991 129 95 12550 11936 0 0 994 1040 559 423 100 100 100 100 24682 24486 1.051 .951 .951 1 1 1 120 836 1 .99 130 6160 25770 122 135 519 532 0 11298 51 11247 .889 11207 11155 1.125 .889 -.169 -.17
19 33161 52575 87 62 33074 52513 35742 55718 103 85 35655 55656 0 0 7025 11121 167 249 100 100 100 100 85587 91311 .63 1.588 1.561 1 1 1 156 952 1 1 140 2090 26020 147 161 112 126 0 49136 58 49078 1.484 52073 52015 .674 1.459 .569 .545
20 36733 58745 89 64 36644 58681 39332 64757 152 134 39243 64693 0 45 7000 11538 1289 1318 100 100 100 100 95325 103936 .624 1.601 1.649 1 1 1 156 869 1 1 140 2330 26020 147 161 136 150 0 54902 60 54842 1.497 60521 60461 .668 1.541 .582 .624

Total number of rows: 4992

Table truncated, full table size 1105 Kbytes.




Supplementary data files not provided
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