Dseq2 gives the same results no matter the condition ???
0
0
Entering edit mode
@bioinformatics-10931
Last seen 2.2 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 • 793 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 837 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6