Hi all,

We are applying Voom normalization to RNA-Seq Counts with the following
code:


library(edgeR)
count <- read.delim("Counts.txt", check.names=FALSE, stringsAsFactors=FALSE)
targets <- read.delim("Targets.txt", check.names=FALSE,
stringsAsFactors=FALSE)

#filter
y <- DGEList(counts=rawdata[,2:31], genes=rawdata[,1:1])
keep <- rowSums(cpm(y)>10) >= 15
y <- y[keep,]
dim (y)

#norm
y <- calcNormFactors(y)

#voom
VST <- voom(y,design=NULL,plot=TRUE)
voom_matrix <- cbind(VST$genes, VST$E)
write.table (voom_matrix, "VOOM_Matrix.txt", sep="\t")


However, I find that even after this filtering step, I am finding negative
expression values within my voom normalized matrix. Why is this?

Michael








-- 
M.S. Breen
PhD, Bioinformatics and Genomics
Clinical and Experimental Sciences
Univ. of Southampton

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