Thank you for the explanation. It was in fact quite obvious.

However, does there arise conceptual problems with comprehending negative
expression values? We know, the cpm is somewhere between 0-1, but does the
log derivative of these numbers cause any down-stream problems?
Differential expression or correlation analysis for example.

Michael


On Tue, Apr 1, 2014 at 6:19 PM, Davis, Wade <davisjwa@health.missouri.edu>wrote:

> Hi Micheal,
> As described in the help file (?voom) the $E component of the output
> object contains a "numeric matrix of normalized expression values on the
> log2 scale".
>
> So negative values indicate low levels of (normalized) expression.
>
> Even though your filtering step filters out genes with 14 or less samples
> (~ half the samples) with cpm >10 you could easily get low levels of
> expression for any particular sample.
>
> Imagine, for a given gene, that half you samples have cpm >10 and the
> other half have cpm=0.1. You would expect to see the later half with
> negative normalized expression levels.
>
> Wade
>
> ________________________________________
> From: Michael Breen [breenbioinformatics@gmail.com]
> Sent: Tuesday, April 01, 2014 4:12 AM
> To: bioconductor@r-project.org
> Subject: [BioC] Voom Normalization and negative numbers
>
> Hi all,
>
> We are applying Voom normalization to RNA-Seq Counts with the following
> code:
>
>
> library(edgeR)
> count <- read.delim("Counts.txt", check.names=FALSE,
> stringsAsFactors=FALSE)
> targets <- read.delim("Targets.txt", check.names=FALSE,
> stringsAsFactors=FALSE)
>
> #filter
> y <- DGEList(counts=rawdata[,2:31], genes=rawdata[,1:1])
> keep <- rowSums(cpm(y)>10) >= 15
> y <- y[keep,]
> dim (y)
>
> #norm
> y <- calcNormFactors(y)
>
> #voom
> VST <- voom(y,design=NULL,plot=TRUE)
> voom_matrix <- cbind(VST$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
>
>         [[alternative HTML version deleted]]
>
>
>


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

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