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Sample GSM90835 Query DataSets for GSM90835
Status Public on Jan 06, 2006
Title 26C Control, t=356hr
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-356, adult liver (pooled, 1 ug poly-A)
Organism Austrofundulus limnaeus
Characteristics CO-356, 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/2002-09/32698.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 33254 39399 148 42 33106 39357 34159 41088 152 47 34011 41046 0 0 4559 5169 47 46 100 100 100 100 72463 75057 .841 1.189 1.207 1 1 1 120 843 1 .99 130 2010 25490 51 64 65 78 0 48641 52 48589 1.468 50726 50674 .681 1.49 .554 .575
2 12883 8075 150 42 12733 8033 12895 8029 176 60 12745 7987 0 0 866 449 185 108 100 100 100 100 20766 20732 1.585 .631 .627 1 1 1 120 850 1 .99 130 2250 25490 51 64 89 102 0 9969 52 9917 .779 9912 9860 1.284 .774 -.361 -.37
3 14833 12498 146 42 14687 12456 15558 13080 190 72 15412 13038 0 0 2534 2056 375 229 100 100 100 100 27143 28450 1.179 .848 .846 1 1 1 120 850 1 .99 130 2490 25490 51 64 113 126 0 15430 52 15378 1.047 16148 16096 .955 1.044 .066 .063
4 1240 641 144 40 1096 601 1274 644 168 56 1130 604 0 0 192 112 315 195 99 100 97 96 1697 1734 1.824 .548 .535 1 1 1 156 967 1 .98 140 2740 25490 51 65 138 152 0 791 49 742 .677 795 746 1.477 .66 -.563 -.6
5 1982 1252 146 41 1836 1211 2056 1295 146 41 1910 1254 0 0 341 202 25 7 100 100 100 100 3047 3164 1.516 .66 .657 1 1 1 156 958 1 .99 140 2990 25480 50 64 163 177 0 1546 51 1495 .814 1599 1548 1.228 .811 -.296 -.303
6 8069 7017 145 41 7924 6976 8409 7392 145 42 8264 7351 0 0 1226 1112 23 7 100 100 100 100 14900 15615 1.136 .88 .89 1 1 1 156 942 1 .99 140 3230 25480 50 64 187 201 0 8663 51 8612 1.087 9126 9075 .92 1.098 .12 .135
7 16175 13813 146 41 16029 13772 17210 14743 148 44 17064 14702 0 0 2852 2366 34 20 100 100 100 100 29801 31766 1.164 .859 .862 1 1 1 120 816 1 .99 130 3470 25480 50 63 211 224 0 17053 51 17002 1.061 18201 18151 .943 1.064 .085 .089
8 1101 580 147 42 954 538 1159 596 149 45 1012 554 0 0 286 159 32 20 100 100 99 100 1492 1566 1.773 .564 .547 1 1 1 156 910 1 .97 140 3710 25490 51 65 235 249 0 716 52 664 .696 736 684 1.436 .676 -.522 -.565
9 392 201 148 45 244 156 367 188 321 59 219 143 0 0 160 80 2666 207 0 27 0 0 400 362 1.564 .639 .653 1 1 1 256 1402 1 .9 180 3950 25470 47 65 257 275 0 248 56 193 .789 232 177 1.267 .806 -.341 -.311
10 9783 7956 152 49 9631 7907 10131 8203 155 50 9979 8154 0 0 1668 1213 28 10 100 100 100 100 17538 18133 1.218 .821 .817 1 1 1 156 913 1 .99 140 4190 25480 50 64 283 297 0 9822 60 9762 1.014 10127 10067 .987 1.009 .019 .013
11 2288 1851 154 50 2134 1801 2288 1850 157 52 2134 1800 0 0 217 153 28 11 100 100 100 100 3935 3934 1.185 .844 .843 1 1 1 120 828 1 .99 130 4430 25480 50 63 307 320 0 2285 62 2223 1.042 2284 2222 .96 1.041 .059 .058
12 1283 668 158 50 1125 618 1276 675 164 53 1118 625 0 0 128 66 62 24 100 100 100 100 1743 1743 1.82 .549 .559 1 1 1 120 828 1 .98 130 4660 25480 50 63 330 343 0 825 62 763 .678 833 772 1.475 .69 -.56 -.535
13 2770 1318 157 50 2613 1268 2746 1311 162 52 2589 1261 0 0 316 117 70 26 100 100 100 100 3881 3850 2.061 .485 .487 1 1 1 120 855 1 .98 130 4900 25480 50 63 354 367 0 1627 62 1565 .599 1619 1557 1.669 .601 -.739 -.734
14 2592 1267 150 47 2442 1220 2731 1337 152 49 2581 1290 0 0 591 261 47 15 100 100 100 100 3662 3871 2.002 .5 .5 1 1 1 156 958 1 .97 140 5150 25480 50 64 379 393 0 1564 58 1506 .617 1651 1593 1.621 .617 -.697 -.697
15 1495 824 145 45 1350 779 1489 814 146 46 1344 769 0 0 130 68 27 9 100 100 100 100 2129 2113 1.733 .577 .572 1 1 1 120 802 1 .98 130 5380 25480 50 63 402 415 0 1017 56 962 .712 1005 949 1.404 .706 -.489 -.501
16 1594 1186 145 45 1449 1141 1667 1256 145 46 1522 1211 0 0 384 243 26 9 100 100 99 100 2590 2733 1.27 .787 .796 1 1 1 156 942 1 .99 140 5620 25480 50 64 426 440 0 1464 56 1409 .972 1551 1495 1.029 .982 -.041 -.026
17 3970 3989 141 45 3829 3944 4248 4253 142 46 4107 4208 0 0 866 851 34 8 100 100 100 100 7773 8315 .971 1.03 1.025 1 1 1 156 943 1 .99 140 5860 25480 50 64 450 464 0 4925 56 4869 1.272 5251 5195 .786 1.265 .347 .339
18 9734 5608 140 45 9594 5563 10049 5812 141 46 9909 5767 0 0 1456 969 23 8 100 100 100 100 15157 15676 1.725 .58 .582 1 1 1 156 1089 1 .99 150 6100 25490 50 65 473 488 0 6923 56 6868 .716 7175 7120 1.397 .719 -.482 -.477
19 26803 36424 150 43 26653 36381 28089 39151 154 46 27939 39108 0 0 5815 8727 43 21 100 100 100 100 63034 67047 .733 1.365 1.4 1 1 1 156 919 1 .99 140 2030 25740 76 90 67 81 0 44968 53 44915 1.685 48335 48281 .593 1.728 .753 .789
20 35401 44180 149 44 35252 44136 37243 46103 161 50 37094 46059 0 0 6099 7669 106 47 100 100 100 100 79388 83153 .799 1.252 1.242 1 1 1 156 886 1 .99 140 2270 25730 75 89 91 105 0 54543 54 54489 1.546 56917 56863 .647 1.533 .628 .616

Total number of rows: 4992

Table truncated, full table size 1106 Kbytes.




Supplementary data files not provided
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