Hi everyone, I am analyzing different RNA seq data from different labs so I want to adjust the batch effects. I am using sva+DESeq2 to plot PCA. But I have a question about the sva settings in RNA seq data analysis. 1. What is the number for n.sv when you conduct this step ( svseq <- svaseq(dat, mod, mod0, n.sv = 2)? 2. People generally use 2. Is it the number of your samples? 3. In sva tutorial, there is a step to estimate the n.sv. But that step is for microarray. Can I just apply the same scripts to get n.sv for my RNA seq data? Thanks in advance.
Question: n.sv number for batch effects in RNA-seq
2.9 years ago by
sophialovechan • 50
sophialovechan • 50 wrote:
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