Dseq2 gives the same results no matter the condition ???

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Bioinformatics ▴ 30

@bioinformatics-10931

Last seen 2.9 years ago

United States

Hello,

I am trying to understand why Dseq2 gives me the same result if I set my condition differently ? I use Raw count values

First way to do

condition <- factor(c(rep("Normal", 10),rep("Tumor", 11)))
dds <- DESeqDataSetFromMatrix(dfm, DataFrame(condition), ~ condition)
keep <- rowSums(counts(dds)) >= 1
dds <- dds[keep,]
dds <- DESeq(dds)

Second way to do

condition <- factor(c(rep("Tumor", 11),rep("Normal", 10)))
dds <- DESeqDataSetFromMatrix(dfm, DataFrame(condition), ~ condition)
keep <- rowSums(counts(dds)) >= 1
dds <- dds[keep,]
dds <- DESeq(dds)

They both give me the same LogFold change???? how is that possible ?

dseq2 • 1.0k views

ADD COMMENT • link 6.5 years ago Bioinformatics ▴ 30

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Entering edit mode

Probably because it is reordering it internally alphabetically or something like that. You could check the source code.

ADD REPLY • link 6.5 years ago chris86 ▴ 420

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