Yuqing Zhang comments

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                                            Yuqing Zhang

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

@Bithorax thanks for your suggestion for the question! Yes, the output will be the dataset corrected by batch effects.

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

@Bithorax Both "group" and "covar_mod" refer to any covariates whose signal you would like to keep in your data. So, in differential expression analysis for example, group would be the...

ComBat-seq + DESeq2 / WGCNA Or DESeq2 (batch as covariate) / ComBat + WGCNA

@Bithorax Unfortunately in real data, we can never be 100% sure that only batch effect is removed, because we do not truly know how batch has affected the data, we...

Implementation with DESeq2 > "invalid class “DESeqDataSet” object: the count data is not in integer mode"

I feel this is more of a question about DESeq2 rather than for combat-seq. Though I'm not the expert here, perhaps converting values in count matrix to integers using as.integer()...

Error in .compressOffsets(y, lib.size = lib.size, offset = offset) : offsets must be finite values

Hi Luca, thank you for providing such detailed error information. It looks like there are samples with only 0 in your data (library size of zero means all gene counts...