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Sample GSM114133 Query DataSets for GSM114133
Status Public on Aug 01, 2006
Title SWES_C065_04-15-03
Sample type RNA
 
Channel 1
Source name EXP: fem-1 mRNA
Organism Caenorhabditis elegans
Characteristics fem-1 mRNA
Extracted molecule polyA RNA
Label CY3
 
Channel 2
Source name REF: reference mRNA
Organism Caenorhabditis elegans
Characteristics reference mRNA
Extracted molecule polyA RNA
Label CY5
 
 
Description 15 hr unc-79;fem-1 vs reference
Data processing log base 2 ratio of cy5 to cy3
 
Submission date Jun 12, 2006
Last update date Jun 13, 2006
Contact name Valerie Reinke
E-mail(s) valerie.reinke@yale.edu
Phone 203-785-5228
Organization name Yale University School of Medicine
Department Genetics
Lab Reinke lab
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL3861
Series (1)
GSE5069 Expression Profiling of MAP Kinase-Mediated Meiotic Progression in C. elegans

Data table header descriptions
ID_REF
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Dia diameter in µm of the feature-indicator
F635 Median median pixel intensity of feature for Cy5 channel
F635 Mean mean pixel intensity of feature for Cy5 channel
F635 SD Cy5 pixel intensity standard deviation
B635 Median median Cy5 feature background intensity
B635 Mean mean Cy5 feature background intensity
B635 SD Cy5 background pixel intensity standard deviation
% > B635+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
% > B635+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635 % Sat percentage of pixel saturation within feature
F532 Median median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Median median feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
% > B532+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
% > B532+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)r
F532 % Sat percentage of feature pixels at wavelength #2 (Cy3) that are saturated
Ratio of Medians ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
Ratio of Means ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
Median of Ratios median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
Mean of Ratios arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
Ratios SD standard deviation of the log of pixel intensity ratios
Rgn Ratio regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn R? coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels number of feature pixels
B Pixels number of background pixels
Sum of Medians sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Sum of Means sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
VALUE Log ratio
F635 Median - B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532 Median - B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635 Mean - B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532 Mean - B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags A value of -100 means that this spot was bad. A value of -75 means that the ID for this spot is empty. A value of -50 means that this spot cannot be aligned during analysis. A value of 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality tests.

Data table
ID_REF X Y Dia F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn R? F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags
1a1b1c 2080 16790 120 5319 5256 3206 119 135 90 89 86 0 7176 7232 4448 113 120 47 90 87 0 0.736 0.722 0.728 0.799 1.873 0.708 0.938 120 585 12263 12256 -0.442 5200 7063 5137 7119 0
1a2b1c 2250 16790 120 1638 1587 713 114 120 61 92 91 0 1749 1649 692 113 115 32 92 90 0 0.932 0.959 0.955 0.955 1.531 0.973 0.924 120 478 3160 3009 -0.102 1524 1636 1473 1536 0
1a3b1c 2420 16790 120 1443 1304 843 112 122 73 75 74 0 1463 1261 721 109 116 40 85 83 0 0.983 1.035 1.030 0.945 1.820 1.123 0.923 120 473 2685 2344 -0.025 1331 1354 1192 1152 0
1a4b1c 2590 16790 120 1942 1785 1108 109 120 69 83 79 0 1948 1858 1046 110 116 44 90 88 0 0.997 0.959 0.972 0.876 2.050 1.034 0.936 120 473 3671 3424 -0.004 1833 1838 1676 1748 0
1a5b1c 2760 16790 120 1515 1363 699 104 119 83 88 86 0 1458 1323 573 104 112 49 90 90 0 1.042 1.033 1.040 1.024 1.846 1.085 0.928 120 489 2765 2478 0.059 1411 1354 1259 1219 0
1a6b1c 2940 16790 120 1446 1384 644 111 124 76 92 90 0 1437 1323 544 102 106 35 94 91 0 1.000 1.043 1.027 1.023 1.449 1.082 0.935 120 498 2670 2494 0.000 1335 1335 1273 1221 0
1a7b1c 3110 16790 120 2578 2455 1160 113 124 70 95 91 0 2349 2140 900 101 105 39 95 92 0 1.097 1.149 1.162 1.139 1.409 1.184 0.938 120 507 4713 4381 0.133 2465 2248 2342 2039 0
1a8b1c 3290 16810 120 1447 1342 729 112 124 80 87 82 0 1501 1268 619 100 107 47 90 89 0 0.953 1.053 1.011 1.014 1.624 1.096 0.924 120 459 2736 2398 -0.070 1335 1401 1230 1168 0
1a9b1c 3440 16810 120 2162 2086 1142 108 116 61 90 86 0 2048 1958 936 100 104 34 95 95 0 1.054 1.065 1.012 0.958 2.256 1.107 0.916 120 463 4002 3836 0.076 2054 1948 1978 1858 0
1a10b1c 3620 16800 130 1669 1568 812 104 121 103 90 86 0 1669 1570 757 99 109 87 90 89 0 0.997 0.995 0.996 0.918 1.850 1.013 0.903 120 536 3135 2935 -0.005 1565 1570 1464 1471 0
1a11b1c 3790 16800 130 7149 7205 3441 105 118 62 100 100 0 6171 6084 2474 101 104 30 100 100 0 1.160 1.187 1.253 1.135 1.809 1.260 0.850 120 495 13114 13083 0.215 7044 6070 7100 5983 0
1a12b1c 3960 16800 140 3121 2896 2090 110 118 60 82 77 0 2753 2472 1597 100 102 28 89 82 0 1.135 1.175 1.190 1.124 1.915 1.245 0.952 156 618 5664 5158 0.183 3011 2653 2786 2372 0
1a13b1c 4130 16800 120 2337 2298 1312 113 120 61 91 90 0 2269 2209 1139 97 101 31 96 93 0 1.024 1.035 1.019 1.031 2.054 1.075 0.945 120 449 4396 4297 0.034 2224 2172 2185 2112 0
1a14b1c 4300 16810 120 2192 2256 1329 107 114 60 89 87 0 2199 2239 1258 102 106 34 95 93 0 0.994 1.006 1.001 0.942 1.942 1.022 0.943 120 436 4182 4286 -0.008 2085 2097 2149 2137 0
1a15b1c 4470 16810 120 3379 3050 1526 114 127 83 94 91 0 4070 3494 1630 104 109 42 95 95 0 0.823 0.866 0.855 0.801 1.916 0.881 0.940 120 441 7231 6326 -0.281 3265 3966 2936 3390 0
1a16b1c 4630 16810 130 2880 2487 1351 119 129 75 90 85 0 2639 2424 1288 106 113 48 95 90 0 1.090 1.022 1.008 0.983 1.474 1.031 0.971 120 519 5294 4686 0.124 2761 2533 2368 2318 0
1a17b1c 4810 16810 120 2796 2612 1187 116 128 67 96 95 0 3155 2983 1212 108 120 68 95 94 0 0.880 0.868 0.872 0.831 1.675 0.891 0.955 120 502 5727 5371 -0.185 2680 3047 2496 2875 0
1a18b1c 4980 16810 120 3613 3823 1793 111 126 78 95 95 0 4290 4526 1981 112 120 54 95 95 0 0.838 0.841 0.885 0.828 1.477 0.858 0.928 120 487 7680 8126 -0.255 3502 4178 3712 4414 0
1a19b1c 5150 16810 130 4812 4864 2743 120 132 82 95 92 0 4785 5511 3091 113 124 80 99 97 0 1.004 0.879 0.885 0.828 1.493 0.880 0.959 120 511 9364 10142 0.006 4692 4672 4744 5398 0
1a20b1c 5300 16820 120 1954 1816 888 113 121 73 94 87 0 1868 1877 897 104 110 41 91 90 0 1.044 0.961 0.993 0.946 1.613 0.964 0.928 120 443 3605 3476 0.062 1841 1764 1703 1773 0

Total number of rows: 19213

Table truncated, full table size 3232 Kbytes.




Supplementary data files not provided

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