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pseudobulk_by apparently dropping columns #23
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I think the problem is that you use the The manual way of forming the pseudo-bulk would look like: splitter <- split(seq_len(ncol(s2)), s2$experimentGroup)
pseudobulk_mat <- do.call(cbind, lapply(splitter, function(idx){
matrixStats::rowSums2(assay(s2), cols = idx)
}))
pseudo_design_mat <- do.call(rbind, lapply(splitter, function(idx){
matrixStats::colMeans2(glmGamPoi.fit$model_matrix, rows = idx)
})) If you look at Best, |
Hi, I am successfully using your package with scRNA-Seq data, but finding a possible bug when trying out the
pseudobulk_by
option. Below I show it working fine withoutpseudobulk_by
and then failing when I add it in:This worked fine. My grouping factor and design matrix looks like this:
Testing for DGE with the following contrast works fine:
... the problem comes when I try to test using
pseudobulk_by
, asHowever by my calculations the aggregated data columns should d be there and are somehow erroneously being dropped, , viz::
I could potentially share the s2 object via ftp if it would help you sleuth this.
Or perhaps you recognize some error on my part?
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