NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90826 Query DataSets for GSM90826
Status Public on Jan 06, 2006
Title Cycle, t=100hr
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-100, adult liver (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics CY-100, 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/2002-07/31117.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 31645 56942 94 67 31551 56875 34547 63295 99 72 34453 63228 0 23 8421 13635 29 27 100 100 100 100 88426 97681 .555 1.803 1.835 1 1 1 156 1005 1 1 140 2070 25740 119 133 110 124 0 47452 56 47396 1.502 52746 52690 .666 1.529 .587 .613
2 25457 14220 95 66 25362 14154 27611 15296 99 70 27516 15230 0 0 5498 2890 26 24 100 100 100 100 39516 42746 1.792 .558 .553 1 1 1 156 937 1 1 140 2310 25740 119 133 134 148 0 11850 55 11795 .465 12747 12692 2.15 .461 -1.104 -1.116
3 24998 30965 95 67 24903 30898 27517 34200 98 70 27422 34133 0 0 5546 6898 18 19 100 100 100 100 55801 61555 .806 1.241 1.245 1 1 1 156 937 1 1 140 2550 25740 119 133 158 172 0 25804 56 25748 1.034 28500 28444 .967 1.037 .048 .053
4 2104 2347 96 72 2008 2275 2097 2372 106 80 2001 2300 0 0 489 539 96 85 100 100 100 100 4283 4301 .883 1.133 1.149 1 1 1 156 937 1 .99 140 2790 25740 119 133 182 196 0 1956 60 1896 .944 1977 1917 1.059 .958 -.083 -.062
5 3625 3885 97 72 3528 3813 3862 4113 107 82 3765 4041 0 0 670 752 41 39 100 100 100 100 7341 7806 .925 1.081 1.073 1 1 1 156 921 1 .99 140 3030 25740 119 133 206 220 0 3238 60 3178 .901 3428 3368 1.11 .894 -.151 -.161
6 20781 30457 97 69 20684 30388 22129 32914 148 135 22032 32845 0 0 5237 8359 833 1101 99 99 98 98 51072 54877 .681 1.469 1.491 1 1 1 156 936 1 1 140 3260 25740 119 133 229 243 0 25381 58 25323 1.224 27428 27371 .817 1.242 .292 .313
7 27413 36741 93 68 27320 36673 29808 39784 98 72 29715 39716 0 0 5684 7903 31 24 100 100 100 100 63993 69431 .745 1.342 1.337 1 1 1 156 953 1 1 140 3510 25740 119 133 254 268 0 30618 57 30561 1.119 33153 33097 .894 1.114 .162 .155
8 2674 2856 90 62 2584 2794 2610 2698 99 69 2520 2636 0 0 771 878 143 89 99 100 99 100 5378 5156 .925 1.081 1.046 1 1 1 156 921 1 .99 140 3750 25740 119 133 278 292 0 2380 52 2328 .901 2248 2197 1.11 .872 -.15 -.198
9 824 801 86 59 738 742 810 747 91 63 724 688 0 0 224 254 26 21 100 100 100 100 1480 1412 .995 1.005 .95 1 1 1 156 988 1 .98 150 3990 25740 118 133 301 316 0 668 49 618 .838 623 573 1.194 .792 -.255 -.337
10 19345 27563 85 58 19260 27505 20138 28769 87 62 20053 28711 0 0 3214 4968 16 21 100 100 100 100 46765 48764 .7 1.428 1.432 1 1 1 156 905 1 1 140 4220 25740 119 133 325 339 0 22969 48 22921 1.19 23974 23926 .84 1.193 .251 .255
11 3025 3048 82 55 2943 2993 3339 3345 83 56 3257 3290 0 0 758 754 10 11 100 100 100 100 5936 6547 .983 1.017 1.01 1 1 1 156 1013 1 1 150 4460 25730 117 132 348 363 0 2540 46 2494 .847 2788 2742 1.18 .842 -.239 -.248
12 2360 2247 82 54 2278 2193 2424 2300 83 56 2342 2246 0 0 573 613 14 14 100 100 100 100 4471 4588 1.039 .963 .959 1 1 1 156 921 1 .99 140 4700 25740 119 133 373 387 0 1873 45 1828 .802 1917 1872 1.247 .799 -.318 -.323
13 4018 2595 81 55 3937 2540 4216 2700 88 58 4135 2645 0 0 663 456 92 41 100 100 100 100 6477 6780 1.55 .645 .64 1 1 1 156 939 1 .99 140 4940 25740 119 133 397 411 0 2163 46 2117 .538 2250 2204 1.86 .533 -.895 -.908
14 4191 4631 83 57 4108 4574 4548 5019 94 64 4465 4962 0 0 898 1008 97 50 100 100 100 100 8682 9427 .898 1.113 1.111 1 1 1 156 928 1 1 140 5180 25730 118 132 421 435 0 3859 48 3812 .928 4183 4135 1.078 .926 -.108 -.111
15 2295 2086 85 59 2210 2027 2426 2192 89 64 2341 2133 0 0 426 368 29 27 100 100 100 100 4237 4474 1.09 .917 .911 1 1 1 156 927 1 .99 140 5420 25730 118 132 445 459 0 1738 49 1689 .764 1827 1778 1.308 .759 -.388 -.397
16 3234 3965 85 59 3149 3906 3460 4271 89 64 3375 4212 0 0 697 879 26 30 100 100 100 100 7055 7587 .806 1.24 1.248 1 1 1 156 927 1 1 140 5660 25730 118 132 469 483 0 3304 49 3255 1.034 3559 3510 .967 1.04 .048 .057
17 7116 6769 86 60 7030 6709 7562 7118 91 63 7476 7058 0 0 1336 1519 26 20 100 100 100 100 13739 14534 1.048 .954 .944 1 1 1 156 927 1 .99 140 5900 25730 118 132 493 507 0 5641 50 5591 .795 5932 5882 1.257 .787 -.33 -.346
18 15745 14695 84 59 15661 14636 16685 15545 88 61 16601 15486 0 0 2786 2462 25 16 100 100 100 100 30297 32087 1.07 .935 .933 1 1 1 156 969 1 1 140 6140 25730 118 132 517 531 0 12246 49 12197 .779 12954 12905 1.284 .777 -.361 -.363
19 37540 61819 95 71 37445 61748 39685 65535 101 79 39590 65464 0 76 6670 9600 33 32 100 100 100 100 99193 105054 .606 1.649 1.654 1 1 1 156 937 1 1 140 2060 25980 143 157 109 123 -100 51516 59 51457 1.374 54613 54553 .728 1.378 .459 .463
20 39470 62520 95 71 39375 62449 41578 65535 102 81 41483 65464 0 79 6099 8634 32 34 100 100 100 100 101824 106947 .631 1.586 1.578 1 1 1 156 853 1 1 140 2300 25980 143 157 133 147 -100 52100 59 52041 1.322 54613 54553 .757 1.315 .402 .395

Total number of rows: 4992

Table truncated, full table size 1110 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap