Wrong number of expansion or contraction Orthogroups #231
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Gamma_branch_probabilities.txt Hi all, |
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Replies: 8 comments
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What number do you think is wrong? |
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For example, when I filter data in Gamma_branch_probabilities.txt, if data lower than 0.05, it should be significantly expanded or contracted, right? However, The filtered results are not consistent with corresponding number in Gamma_clade_results.txt, that's what I said wrong number. Actually ,all my objective is simple, I wanna know which Orthogroups are expanded or contracted in each species, what's the result files I should focus on (My results files generated by CAFE5), thanks for your patient replay! |
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The counts of Gamma_change.tab are consistent with that of Gamma_clade_results.txt, but not with that of Gamma_family_results.txt(significantly expanded/contracted OGs were much less than that of Gamma_clade_results.txt or Gamma_change.tab) |
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if OGs with P-value lower than 0.05 were considered as significantly expanded or contracted, which is consistent with 'Gamma_branch_probabilities.tab' and 'Gamma_family_results.txt' seemly. However, if based on this criteria, much less significantly OGs were found comparing to 'Gamma_change.tab' or 'Gamma_clade_results.txt'. So I am confused what should I believe, My objective is pick which OGs were significantly expanded or contracted in each species and their corresponding MRCA. |
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You can use the branch probabilities for that task. The family-wide P-values only represent the probability of the family as a whole across the entire tree, and thus don't necessarily have any bearing on whether a particular branch in the tree is significant or not. |
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Hi, I am also trying to identify the underlying orthogroups behind a branch expansion. I am confused how the different output files integrate, for example in Base_clade_results.txt |
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You are correct - the clade_results file is a count of all expansions, not just those marked as significant. |
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You can use the branch probabilities for that task. The family-wide P-values only represent the probability of the family as a whole across the entire tree, and thus don't necessarily have any bearing on whether a particular branch in the tree is significant or not.