Question

Deseq normalization with adjusting gene length

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Maryam • 0

@maryam-17785

Last seen 6.1 years ago

Hi all,
I asked the question in Biostar and then I got the answer that I should use deseq2 normalization with gene length adjustment. Is it possible to use deseq2 normalization with gene length adjustment like as FPKM gene length adjustment? I have 250 samples from healthy and disease states and I want to integrate gene expression with metabolic model. Indeed, I need within sample normalization (adjusting gene length) and between sample normalization(Deseq2). Because FPKM is not a good normalization in cross-sample analysis I want to use deseq2 normalization but i should account gene length in the normalization too.

Any help appreciated

deseq2 normalization • 2.7k views

ADD COMMENT • link 6.1 years ago Maryam • 0

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Here is the R code for whoever needs it.

cts <- as.matrix(read.csv("Count_data.txt", row.names = 1, header= TRUE, sep="\t"))
coldata <- read.csv("coldata.txt", row.names = 1, sep="\t")
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design =  ~ condition)
txdb <- makeTxDbFromGFF("gencode.v19.annotation.gtf_withproteinids", format="gtf", circ_seqs=character())
ebg <- exonsBy(txdb, by="gene")
rowRanges(dds) = GRangesList(ebg)
FPKM = fpkm(dds)

ADD REPLY • link 6.1 years ago Maryam • 0

score 2 · Accepted Answer · 2018-12-12

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Michael Love 43k

@mikelove

Last seen 1 day ago

United States

We have an fpkm() function which does just this, but you need to provide the exons or the basepairs. See the function help page.

ADD COMMENT • link 6.1 years ago Michael Love 43k

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Thanks Michael, but I do not want FPKM. I need deseq2 normalization which accounts gene length in normalization too. Is it possible?

ADD REPLY • link 6.1 years ago Maryam • 0

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Again, this is what our function fpkm() does and you should read the help page for that function.