I want to create the normalized read count with the RLE method from edgeR or DESeq.
Below is the commands am using to normalize my raw read count for edgeR suite with RLE, but how to output that matrix with normalized counts? Am unable to find the object for which the table has to be called.
library(edgeR) x <- read.delim("my_path/raw_counts.txt",row.names="symbol") ## filtering genes with low expression so filtering gene with a normal read count less than 50 keep <- rowSums(x)>50 x <- x[keep,] dim(x) norm_factors=calcNormFactors(as.matrix(x),method="RLE") group <- c(rep("A",24),rep("B",25),rep("C",23)) y <- DGEList(counts=x,group=group,norm.factors=norm_factors) design <- model.matrix(~group)
Now I want to extract the normalized count matrix from here. How do I do that?
Also the default normalization in DESeq is RLE method. I want to extract the normalized matrix by DESeq, by any one method I want to get the normalized matrix? how do I do that? below is the DESeq code
cds<-newCountDataSet(x, c(rep("A",25),rep("B",24),rep("C",23))) disp<-estimateSizeFactors(cds) disp1<-estimateDispersions(disp)
How do I now extract the matrix of normalized counts for my samples?
So can anyone help me how I can extract the normalized read count matrix from the above methods? It would be very helpful for me then.