Differential expression using Scran batch corrected data
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3.5 years ago

Hi, guys

I intend to to integrate two single-cell RNA-Seq datasets and then correct their expression values for batch effect using Scran mnnCorrect function. However, after mnn correction, the output is a matrix which includes logtransformed and negative values. Since softwares usually require raw count data for differential expression (Deseq2 for example) I am looking for a way to perform the analysis after the integration and correction for batch effect. Do you have any kind of suggestion or guidelines on how could I proceed? Thanks in advance!

RNA-Seq single-cell Scran Batch correction • 1.4k views
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