combat-Seq error
I'm running combat-seq, but receiving the following error message:
Error in sva::ComBat_seq(count_matrix, batch = batches, group = groups) :
The covariate is confounded with batch! Remove the covariate and rerun ComBat-Seq
Can you help me out?
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ATpoint
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pinheirofabiano •
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pinheirofabiano •
1 answer
Without any more information on what your batches and groups are we can't really suggest much more but the error message is quite clear: your batches are confounded with the covariate which means that removing batch effect will likely remove biological differences.
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yura.grabovska •
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