Hi,
I intend to run RNA-seq analysis using DESeq package. But since I am working on TMM normalization method I wanted to run DESeq with TMM as well. I wanted to ask if it is enough if I pass the "norm.factors" obtained from "calcNormFactors" from edgeR to "sizeFactor" of DESeq. Or I should multiply the "norm.factors" by library size and then passed it to DESeq?
Or do you think it is meaningful or not?
So either of these:
OR:
Thanks in advance
I intend to run RNA-seq analysis using DESeq package. But since I am working on TMM normalization method I wanted to run DESeq with TMM as well. I wanted to ask if it is enough if I pass the "norm.factors" obtained from "calcNormFactors" from edgeR to "sizeFactor" of DESeq. Or I should multiply the "norm.factors" by library size and then passed it to DESeq?
Or do you think it is meaningful or not?
So either of these:
Code:
normFactor <- calcNormFactors(countTable) scale <- countTable$samples$lib.size*countTable$samples$norm.factors cds <- newCountDataSet(countTable, conditions) pData(cds)$sizeFactor <- scale
Code:
normFactor <- calcNormFactors(countTable) cds <- newCountDataSet(countTable, conditions) pData(cds)$sizeFactor <- normFactor