Hello: I am using DEseq2 for Small RNA-seq data. I have four replicates for control and two replicates for treated. I want to see differential expression of different kinds of loci (like expression of all gypsy elements in control vs treated). But I want to normalize my two datasets using All ribosomal RNAs across the two samples (I have small RNAs generated from ribosomal RNA in both of my samples). Any idea how to do that? I am using these commands:
> countTable = read.table("ABC.txt") > condition = factor(c("un", "un", "un", "un", "t", "t")) > library ("DESeq") >cds = newCountDataSet(CountTable, condition ) >estimateSizeFactors(cds[which(cds$feature=="rRNA")]) >sizeFactors( cds ) >head(counts( cds, normalized=TRUE))
But when I use: sizeFactors( cds ) command, I get this error:
un1 un2 un3 un4 t1 t2 NA NA NA NA NA NA
Please help me out!