[BioC] Voom Normalization and negative numbers

[Pekka Kohonen]

Dear Michael,

Could this be because some counts (after normalization) are less than
1? And log of a number > 0 and < 1 is a negative number?

Best, Pekka

2014-04-01 10:12 GMT+01:00 Michael Breen <breenbioinformatics at gmail.com>:
> 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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>
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