NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM71132 Query DataSets for GSM71132
Status Public on Aug 20, 2005
Title L1 MTC#3T2 (red, channel 2) vs. RefB-JW (green, channel 1)
Sample type RNA
 
Channel 1
Source name RefB-JW (green)
Organism Caenorhabditis elegans
Characteristics RefB-JW (green)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name L1 MTC#3T2 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#3T2 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13872.gif
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 Aug 19, 2005
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 GPL2754
Series (1)
GSE3169 Global analysis of dauer gene expression in Caenorhabditis elegans

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 14780 11996 89 107 14691 11889 13952 8821 100 120 13863 8714 0 0 10063 9671 86 95 100 100 100 100 26580 22577 1.236 .809 .629 .751 .81 .288 80 366 .843 .97 100 2060 18950 42 52 37 47 0 12923 115 12808 .872 9503 9387 1.147 .677 -.198 -.562
2 4431 21625 81 105 4350 21520 5271 24986 97 124 5190 24881 0 0 1977 10850 62 102 99 100 98 100 25870 30071 .202 4.947 4.794 5.773 5.067 5.993 120 544 4.98 .98 120 2240 18970 43 55 54 66 0 23296 113 23183 5.329 26917 26804 .188 5.165 2.414 2.369
3 613 1386 74 91 539 1295 611 1429 77 94 537 1338 0 0 154 563 19 24 100 100 100 100 1834 1875 .416 2.403 2.492 2.349 2.385 .773 52 261 2.403 .95 80 2410 18960 44 52 73 81 0 1493 98 1395 2.588 1539 1441 .386 2.684 1.372 1.424
4 12424 9410 80 96 12344 9314 14343 11146 88 103 14263 11050 0 0 4377 3429 39 43 100 100 100 100 21658 25313 1.325 .755 .775 .799 .766 .323 52 359 .741 .98 90 2560 18960 43 52 87 96 0 10137 103 10034 .813 12007 11904 1.23 .835 -.299 -.261
5 20011 2683 85 101 19926 2582 22600 2862 94 108 22515 2761 0 0 6200 736 57 44 100 100 100 100 22508 25276 7.717 .13 .123 .139 .129 .05 52 292 .125 .98 80 2750 18960 44 52 107 115 0 2890 109 2782 .14 3083 2974 7.164 .132 -2.841 -2.92
6 690 692 83 111 607 581 355 472 94 125 272 361 0 0 617 410 43 49 98 100 92 100 1188 633 1.045 .957 1.327 1.529 1.274 .89 52 280 .741 .94 80 2910 18960 44 52 123 131 0 745 120 626 1.031 508 389 .97 1.43 .044 .516
7 13194 5824 209 169 12985 5655 14466 6951 246 187 14257 6782 0 0 5528 2928 277 74 100 100 100 100 18640 21039 2.296 .436 .476 .421 .426 .123 80 476 .444 .98 110 3070 18970 43 54 137 148 0 6274 182 6092 .469 7488 7306 2.131 .512 -1.092 -.964
8 1863 1544 198 183 1665 1361 1903 1562 256 201 1705 1379 0 0 578 382 154 69 100 100 98 100 3026 3084 1.223 .817 .809 .871 .824 .26 52 264 .756 .95 80 3220 18970 45 53 154 162 0 1663 197 1466 .881 1683 1486 1.136 .871 -.183 -.199
9 42975 4370 159 139 42816 4231 49811 4829 201 147 49652 4690 0 0 15523 1701 167 50 100 100 100 100 47047 54342 10.12 .099 .094 .104 .096 .048 80 420 .095 .95 100 3390 18970 44 54 170 180 0 4708 150 4558 .106 5202 5052 9.394 .102 -3.232 -3.297
10 3081 2881 120 124 2961 2757 3278 3032 141 138 3158 2908 0 0 726 782 69 61 100 100 100 100 5718 6066 1.074 .931 .921 .927 .924 .149 52 335 .914 .98 90 3550 18960 43 52 186 195 0 3104 134 2970 1.003 3266 3133 .997 .992 .004 -.012
11 21610 20685 125 133 21485 20552 24246 24224 168 153 24121 24091 0 0 6684 8366 127 65 100 100 100 100 42037 48212 1.045 .957 .999 .921 .992 .212 80 473 .98 .98 110 3710 18970 43 54 201 212 0 22284 143 22140 1.031 26096 25953 .97 1.076 .043 .106
12 2034 8865 101 124 1933 8741 2373 10681 114 128 2272 10557 0 0 815 3756 55 36 100 100 100 100 10674 12829 .221 4.522 4.647 4.64 4.569 1.242 80 381 4.469 .99 100 3870 18960 43 53 218 228 0 9550 134 9417 4.871 11507 11373 .205 5.006 2.284 2.324
13 420 1055 82 112 338 943 316 1015 85 114 234 903 0 0 515 293 24 28 100 100 100 100 1281 1137 .358 2.79 3.859 4.501 4.028 2.774 52 350 1.053 .67 90 4020 18970 44 53 233 242 0 1137 121 1016 3.006 1093 973 .333 4.157 1.588 2.056
14 678 1031 76 109 602 922 641 936 81 111 565 827 0 0 250 488 21 26 100 100 100 100 1524 1392 .653 1.532 1.464 1.604 1.526 .749 52 297 1.488 .93 80 4200 18970 45 53 252 260 0 1111 117 993 1.65 1008 891 .606 1.577 .722 .657
15 1730 1637 83 114 1647 1523 1675 1589 87 116 1592 1475 0 0 356 235 27 28 100 100 100 100 3170 3067 1.081 .925 .927 .964 .934 .24 52 290 .852 .96 80 4350 18970 45 53 267 275 0 1764 123 1641 .996 1712 1589 1.004 .998 -.006 -.003
16 1466 1758 84 112 1382 1646 1543 1841 87 114 1459 1729 0 0 291 370 26 28 100 100 100 100 3028 3188 .84 1.191 1.185 1.227 1.165 .339 52 352 1.16 .97 90 4520 18970 44 53 283 292 0 1894 121 1773 1.283 1983 1863 .779 1.277 .36 .352
17 14224 21108 79 112 14145 20996 16057 23489 84 116 15978 23377 0 0 5109 6790 47 49 100 100 100 100 35141 39355 .674 1.484 1.463 1.724 1.454 .975 52 346 1.42 .98 90 4670 18960 43 52 298 307 0 22739 121 22619 1.599 25304 25184 .625 1.576 .677 .656
18 712 896 71 104 641 792 712 897 73 106 641 793 0 0 151 167 20 24 100 100 100 100 1433 1434 .809 1.236 1.237 1.288 1.215 .342 52 354 1.148 .93 90 4830 18970 44 53 314 323 0 965 112 853 1.331 966 854 .751 1.333 .413 .414
19 3818 4903 69 102 3749 4801 4443 5757 72 104 4374 5655 0 0 1406 1929 20 23 100 100 100 100 8550 10029 .781 1.281 1.293 1.3 1.3 .355 80 489 1.259 .98 110 5000 18960 42 53 330 341 0 5282 110 5172 1.38 6202 6092 .725 1.393 .464 .478
20 7412 2742 71 103 7341 2639 8283 2951 75 105 8212 2848 0 0 2053 802 24 24 100 100 100 100 9980 11060 2.782 .359 .347 .363 .36 .079 80 393 .353 .98 100 5160 18970 44 54 347 357 0 2954 111 2843 .387 3179 3068 2.582 .374 -1.369 -1.42

Total number of rows: 21504

Table truncated, full table size 4779 Kbytes.




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