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Sample GSM70919 Query DataSets for GSM70919
Status Public on Aug 20, 2005
Title L1 MTC#1T6 (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#1T6 (red)
Organism Caenorhabditis elegans
Characteristics L1 MTC#1T6 (red)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Development, L1
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13800.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 18, 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 GPL2653
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 14257 7991 96 77 14161 7914 15719 8480 104 84 15623 8403 0 0 5930 2897 83 42 100 100 100 100 22075 24026 1.789 .559 .538 .597 .566 .17 80 553 .534 .95 110 1640 16640 46 57 74 85 0 6707 65 6643 .469 7118 7053 2.132 .451 -1.092 -1.147
2 5398 7022 102 79 5296 6943 5641 7151 109 86 5539 7072 0 0 1737 1925 80 39 100 100 100 100 12239 12611 .763 1.311 1.277 1.561 1.305 1.133 52 306 1.206 .95 80 1820 16650 49 57 94 102 0 5894 66 5828 1.1 6002 5936 .909 1.072 .138 .1
3 693 813 100 79 593 734 727 797 102 83 627 718 0 0 164 160 24 24 100 100 98 100 1327 1345 .808 1.238 1.145 1.421 1.232 .842 52 251 1.124 .93 80 1990 16650 49 57 111 119 0 682 66 616 1.039 669 603 .963 .961 .055 -.057
4 7394 7200 91 83 7303 7117 7055 7077 95 86 6964 6994 0 0 5641 5278 29 32 100 100 100 100 14420 13958 1.026 .975 1.004 1.096 .962 .499 80 509 .914 .96 110 2130 16620 44 55 123 134 0 6043 70 5974 .818 5940 5871 1.223 .843 -.29 -.246
5 15534 6304 90 83 15444 6221 19969 6920 94 85 19879 6837 0 0 8634 2923 37 32 100 100 100 100 21665 26716 2.483 .403 .344 .688 .391 .957 80 446 .363 .94 100 2310 16650 48 58 142 152 0 5291 70 5222 .338 5808 5739 2.958 .289 -1.564 -1.792
6 2272 977 89 80 2183 897 1893 861 91 81 1804 781 0 0 1762 586 21 18 100 100 100 100 3080 2585 2.434 .411 .433 .781 .432 .914 32 176 .341 .91 60 2470 16630 48 54 160 166 0 820 67 753 .345 723 656 2.899 .363 -1.536 -1.46
7 8780 3748 91 79 8689 3669 10655 4301 94 81 10564 4222 0 0 5372 2149 22 19 100 100 100 100 12358 14786 2.368 .422 .4 .549 .416 .458 80 435 .397 .96 100 2630 16640 47 57 174 184 0 3146 66 3080 .354 3610 3544 2.821 .335 -1.496 -1.576
8 1450 899 96 80 1354 819 1107 838 99 82 1011 758 0 0 1158 574 24 18 100 100 100 100 2173 1769 1.653 .605 .75 .921 .563 .884 32 218 .498 .9 70 2780 16630 47 54 190 197 0 755 67 687 .508 703 636 1.97 .629 -.978 -.668
9 40809 1982 93 85 40716 1897 49288 1939 108 96 49195 1854 7 0 20333 1039 97 85 100 96 100 92 42613 51049 21.463 .047 .038 .054 .045 .037 80 446 .045 .95 100 2950 16640 47 57 206 216 0 1664 71 1592 .039 1628 1556 25.571 .032 -4.676 -4.982
10 3147 2034 91 82 3056 1952 3496 2202 111 109 3405 2120 0 0 1518 732 118 126 100 100 98 100 5008 5525 1.566 .639 .623 .834 .646 .632 52 293 .55 .95 90 3120 16630 46 55 223 232 0 1707 69 1638 .536 1848 1779 1.865 .523 -.899 -.936
11 19981 20088 90 79 19891 20009 16595 15951 96 95 16505 15872 0 0 13609 12857 66 143 98 100 98 99 39900 32377 .994 1.006 .962 2.393 .964 5.809 120 477 .94 .96 120 3260 16640 46 58 236 248 0 16861 66 16795 .844 13389 13322 1.184 .807 -.244 -.309
12 1521 2173 88 78 1433 2095 1520 2256 91 79 1432 2178 0 0 1054 1331 22 18 98 100 93 100 3528 3610 .684 1.462 1.521 2.727 1.523 4.792 80 412 1.307 .94 100 3430 16630 46 56 254 264 0 1824 65 1758 1.227 1894 1828 .815 1.277 .295 .352
13 14978 14491 90 78 14888 14413 14846 12603 93 80 14756 12525 0 0 9735 8038 24 19 100 100 100 100 29301 27281 1.033 .968 .849 1.638 1.033 2.272 32 231 .863 .94 70 3590 16620 46 53 271 278 0 12163 65 12098 .813 10579 10513 1.231 .712 -.299 -.489
14 942 1025 88 80 854 945 1044 1065 99 93 956 985 0 0 389 372 74 81 94 98 94 96 1799 1941 .904 1.107 1.03 1.888 1.072 3.941 52 364 1.017 .94 90 3750 16620 45 54 286 295 0 860 67 793 .929 894 827 1.077 .865 -.107 -.21
15 4274 3673 90 84 4184 3589 4147 3824 102 98 4057 3740 0 0 3337 2581 75 82 100 100 98 98 7773 7797 1.166 .858 .922 1.149 .878 .95 80 435 .773 .94 100 3920 16630 46 56 303 313 0 3083 71 3012 .72 3210 3139 1.389 .774 -.474 -.37
16 1863 2095 89 79 1774 2016 2077 2345 94 86 1988 2266 0 0 780 759 55 47 100 100 100 100 3790 4254 .88 1.136 1.14 1.28 1.137 .598 80 385 1.055 .96 110 4080 16630 45 56 318 329 0 1758 66 1692 .954 1968 1902 1.048 .957 -.068 -.064
17 15037 32601 87 79 14950 32522 9115 26164 90 82 9028 26085 0 23 12830 25588 22 20 99 100 99 100 47472 35113 .46 2.175 2.889 5.152 2.128 13.953 120 537 2.028 .97 120 4230 16610 43 55 333 345 0 27364 66 27298 1.826 21961 21895 .548 2.425 .869 1.278
18 1093 1491 86 81 1007 1410 1114 1520 92 85 1028 1439 0 0 367 475 33 32 100 100 98 100 2417 2467 .714 1.4 1.4 1.726 1.44 1.549 52 331 1.279 .94 90 4400 16620 45 54 351 360 0 1252 68 1184 1.175 1276 1208 .851 1.175 .233 .233
19 5186 6372 87 80 5099 6292 5683 7434 93 84 5596 7354 0 0 2983 3248 33 29 100 100 100 100 11391 12950 .81 1.234 1.314 1.6 1.234 1.319 80 427 1.133 .95 100 4570 16620 45 55 368 378 0 5348 67 5281 1.036 6240 6173 .965 1.103 .051 .142
20 10460 2953 86 79 10374 2874 11717 3389 89 81 11631 3310 0 0 4824 1253 19 17 100 100 100 100 13248 14941 3.61 .277 .285 .351 .268 .342 80 391 .26 .96 100 4730 16620 45 55 384 394 0 2479 66 2412 .233 2845 2778 4.3 .239 -2.104 -2.066

Total number of rows: 21504

Table truncated, full table size 4752 Kbytes.




Supplementary data files not provided
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