Variance stabilized values and batch correction
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le2336 ▴ 20
@le2336-10789
Last seen 2.1 years ago

I am interested in using variance stabilized values of my data (that are the outputs of DESeq2's varianceStabilizingTransformation function) for machine learning and other applications. I ran the following:

dds <- DESeqDataSetFromMatrix(countData = counts, colData = metadata, design = ~Institution + Condition)
vsd <- varianceStabilizingTransformation(dds, blind = FALSE)


Although I tried to include the batch (Institution) in the design argument, I still see batches in my PCA plot. This section of the vignette described a solution for this that I have pasted below:

mat <- assay(vsd)
mat <- limma::removeBatchEffect(mat, vsd\$batch)
assay(vsd) <- mat
plotPCA(vsd)


Can the output of removeBatchEffect in this code now be used for all other downstream applications, and not just for visualization?

Thanks very much.

deseq2 vst • 526 views
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@mikelove
Last seen 5 days ago
United States

Yes, I have used this kind of workflow to remove unwanted variation from VST data.

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Thank you for the clarification!