Dseq2 gives the same results no matter the condition ???
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Entering edit mode
@bioinformatics-10931
Last seen 10 months 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 • 461 views
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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.

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