Table 2 |
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Accuracy of allele frequency estimation for DNA pools. |
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|
Correction methoda |
Allele frequency difference (Pools - Individual samples) |
Absolute valuesb |
% of SNPs with over-estimated allele frequencyc |
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|
|
|
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|
Sample group |
Mean difference |
SD |
Mean difference |
SD |
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|
|
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|
1 |
Case |
0.0726 |
0.0414 |
0.0728 |
0.0411 |
99.1 |
|
2 |
Case |
0.0725 |
0.0419 |
0.0725 |
0.0418 |
99.1 |
|
3 |
Case |
0.0477 |
0.0435 |
0.0487 |
0.0423 |
94.3 |
|
4 |
Case |
0.0690 |
0.0511 |
0.0740 |
0.0435 |
92.6 |
|
1 |
Control |
0.0627 |
0.0467 |
0.0630 |
0.0463 |
99.1 |
|
2 |
Control |
0.0625 |
0.0465 |
0.0626 |
0.0463 |
99.1 |
|
3 |
Control |
0.0352 |
0.0512 |
0.0389 |
0.0484 |
85.7 |
|
4 |
Control |
0.0591 |
0.0500 |
0.0637 |
0.0438 |
93.5 |
|
1 |
Case - Control |
0.0099 |
0.0276 |
0.0246 |
0.0158 |
70.4 |
|
2 |
Case - Control |
0.0100 |
0.0275 |
0.0247 |
0.0157 |
69.4 |
|
3 |
Case - Control |
0.0125 |
0.0328 |
0.0298 |
0.0184 |
68.6 |
|
4 |
Case - Control |
0.0099 |
0.0293 |
0.0253 |
0.0176 |
69.4 |
|
|
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|
a Correction methods used include those based on (1) Hoogendoorn et al [6], (2) Meaburn et al [7], (3) Craig et al [8] plus Meaburn et al [7], and (4) no adjustment. b Mean of the absolute values for the differences in allele frequencies between DNA pools and individual samples. c In total, 108 SNPs were compared for allele frequency differences as estimated for DNA pools and individual DNA samples. However, only 105 SNPs were compared for the correction method (3) (Craig et al [8] plus Meaburn et al [7]) because 3 SNPs were filtered out. |
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|
Ho et al. BMC Genetics 2012 13:1 doi:10.1186/1471-2156-13-1 |
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