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Sample GSM91446 Query DataSets for GSM91446
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. fer-15 day 9 (8/12/00)
Sample type RNA
 
Channel 1
Source name fer-15 day 9 (8/12/00)
Organism Caenorhabditis elegans
Characteristics fer-15 day 9 (8/12/00)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 ref. JL1
Organism Caenorhabditis elegans
Characteristics N2 ref. JL1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: aging, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13704.gif
Measurement: time(absolute) 10 d
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 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2653
Series (1)
GSE4005 Aging time course

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 2608 4843 161 88 2447 4755 2716 5358 176 166 2555 5270 0 0 628 1134 68 161 100 100 100 100 7202 7825 .515 1.943 2.063 1.964 1.966 1.343 32 230 1.963 .96 70 2340 19900 54 61 102 109 0 3343 61 3282 1.341 3699 3638 .746 1.424 .424 .51
2 1293 3636 159 96 1134 3540 1471 4306 170 151 1312 4210 0 0 520 1352 64 137 92 100 92 100 4674 5522 .32 3.122 3.209 3.09 3.095 1.415 80 484 3.036 .96 100 2510 19900 53 63 118 128 0 2510 66 2444 2.155 2972 2906 .464 2.215 1.108 1.147
3 594 692 140 69 454 623 554 578 146 70 414 509 0 0 345 502 45 18 93 100 87 100 1077 923 .729 1.372 1.229 1.264 1.2 1.801 32 232 1.451 .9 70 2690 19900 54 61 137 144 0 478 48 430 .947 399 351 1.056 .849 -.078 -.237
4 3931 2536 139 75 3792 2461 3997 2031 147 76 3858 1956 0 0 2554 1468 47 20 100 100 100 100 6253 5814 1.541 .649 .507 .788 .658 2.613 12 98 .6 .92 50 2820 19890 54 59 151 156 0 1751 52 1699 .448 1402 1350 2.232 .35 -1.158 -1.515
5 887 4389 159 78 728 4311 788 4029 163 82 629 3951 0 0 595 3620 55 26 84 100 78 100 5039 4580 .169 5.922 6.281 5.522 5.948 1.733 32 176 6.337 .94 60 2970 19910 56 62 166 172 0 3030 54 2976 4.088 2781 2727 .245 4.336 2.031 2.116
6 283 290 153 69 130 221 251 275 156 74 98 206 0 0 110 198 43 31 83 83 58 66 351 304 .588 1.7 2.102 1.714 1.687 3.26 12 104 1.764 .57 50 3150 19900 55 60 184 189 0 200 48 153 1.173 190 142 .852 1.451 .231 .537
7 2402 5640 151 73 2251 5567 2542 6234 157 79 2391 6161 0 0 1320 3062 48 30 100 100 96 100 7818 8552 .404 2.473 2.577 2.842 2.636 1.722 32 236 2.517 .95 70 3310 19890 53 60 199 206 0 3893 50 3843 1.707 4303 4253 .586 1.779 .772 .831
8 479 397 167 86 312 311 443 416 191 108 276 330 0 0 99 66 115 71 100 100 91 100 623 606 1.003 .997 1.196 1.019 1.117 1.322 12 104 .927 .85 50 3450 19890 54 59 214 219 0 274 59 215 .688 287 228 1.453 .825 -.539 -.277
9 56493 7808 235 107 56258 7701 59007 8231 2323 347 58772 8124 1 0 10598 1843 4254 498 100 100 100 100 63959 66896 7.305 .137 .138 .135 .142 1.279 52 326 .134 .95 80 3620 19900 54 62 230 238 0 5390 74 5316 .094 5682 5608 10.583 .095 -3.404 -3.39
10 1394 2402 1884 503 -490 1899 1393 2372 4043 653 -491 1869 0 0 190 285 4687 453 0 100 0 100 1409 1378 null null null 0 0 1 32 236 20.892 .14 70 3790 19890 53 60 247 254 0 1658 347 1311 null 1637 1290 null null null null
11 11656 5431 219 103 11437 5328 11541 5488 601 266 11322 5385 0 0 1185 366 957 417 100 100 100 100 16765 16707 2.147 .466 .476 .467 .47 1.1 32 232 .435 .96 70 3940 19900 54 61 262 269 0 3749 71 3678 .322 3788 3717 3.11 .328 -1.637 -1.607
12 938 1766 144 80 794 1686 946 1809 230 124 802 1729 0 0 142 353 645 300 84 100 0 100 2480 2531 .471 2.123 2.156 2.095 2.244 1.37 52 373 2.242 .93 90 4100 19900 53 62 277 286 0 1219 55 1164 1.466 1249 1193 .682 1.488 .552 .574
13 2922 1900 136 76 2786 1824 1679 1195 139 87 1543 1119 0 0 3951 1902 40 71 83 100 83 91 4610 2662 1.527 .655 .725 1.216 .815 3.647 12 104 .503 .88 50 4260 19890 54 59 295 300 0 1312 52 1259 .452 825 772 2.213 .501 -1.146 -.998
14 777 1072 146 72 631 1000 849 1050 148 75 703 978 0 0 233 495 35 24 100 100 100 100 1631 1681 .631 1.585 1.391 1.471 1.479 1.458 12 68 1.73 .9 40 4420 19900 56 60 312 316 0 740 50 690 1.094 725 675 .914 .96 .13 -.058
15 738 902 154 70 584 832 788 950 156 74 634 880 0 0 397 435 50 21 91 100 83 100 1416 1514 .702 1.425 1.388 1.801 1.441 2.567 12 104 1.338 .9 50 4570 19890 54 59 326 331 0 623 48 574 .983 656 607 1.017 .958 -.024 -.062
16 1039 977 139 68 900 909 924 1028 143 69 785 960 0 0 527 581 43 17 100 96 100 96 1809 1745 .99 1.01 1.223 .884 .985 2.014 32 176 1.04 .94 60 4740 19900 55 61 343 349 0 674 47 627 .697 710 663 1.434 .844 -.52 -.244
17 4829 4310 139 76 4690 4234 5565 3933 148 79 5426 3857 0 0 3763 2754 50 22 100 100 100 100 8924 9283 1.108 .903 .711 1.334 .839 2.674 12 104 .812 .94 50 4890 19890 54 59 358 363 0 2975 52 2923 .623 2715 2662 1.605 .491 -.682 -1.027
18 972 1109 142 77 830 1032 1068 1046 148 79 926 969 0 0 555 641 43 23 87 100 84 100 1862 1895 .804 1.243 1.046 1.493 1.374 2.033 32 170 1.234 .94 60 5060 19890 54 60 375 381 0 766 53 712 .858 722 669 1.165 .722 -.22 -.469
19 1625 2600 135 67 1490 2533 1712 2287 140 69 1577 2220 0 0 748 1345 44 17 100 100 100 100 4023 3797 .588 1.7 1.408 1.706 1.81 1.444 32 170 1.769 .94 60 5220 19890 54 60 391 397 0 1795 46 1748 1.173 1579 1532 .852 .972 .231 -.041
20 13448 4448 170 77 13278 4371 14694 4567 242 95 14524 4490 0 0 3912 540 241 59 100 100 100 100 17649 19014 3.038 .329 .309 .366 .314 1.752 52 372 .289 .94 90 5380 19890 52 61 405 414 0 3070 53 3017 .227 3153 3099 4.401 .213 -2.138 -2.228

Total number of rows: 21504

Table truncated, full table size 4802 Kbytes.




Supplementary data files not provided
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