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Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE by Hervé Pagès 16k

See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932

Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE by Hervé Pagès 16k

See https://github.com/Bioconductor/GenomeInfoDb/issues/82#issuecomment-1409482932

Comment: Sva and batch effect by Gordon Smyth 47k

(+1). I find that ComBat tends to introduce spurious differential expression so, you think there's a batch effect affecting the variances a…

Comment: Advice for the analysis of microarray data with limma by Gordon Smyth 47k

You mean references on orthogonal polynomials? Polynomial approximation is a classic topic in mathematics and statistics and there are many…

Comment: Limma-voom with inverse probability weights (similar to sample weights) by Gordon Smyth 47k

The potential problem isn't with empirical Bayes with the fact that the variance estimate from your method A linear model might not be mean…

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Answer: Sva and batch effect

Answer: Limma-voom with inverse probability weights

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