Hello,
I am using DESeq2 for differential expression analysis of RNA Seq data.
My question is: which is considered "control" or "treated" in the "countData" and "condition" table.
Let me explain.
When having "countData" table in the format of "control" "control" "control" "control" "treated" "treated" "treated" "treated" table, a also assign the "condition" as follows:
condition <- factor(c(rep("control", 4), rep("treat", 4)))
Following analysis, I reach to the
res <- results(dds)
and
head(res) gives
log2 fold change (MAP): condition treat vs ctrl
Wald test p-value: condition treat vs ctrl
The exact same result I get when I reverse the "condition":
condition <- factor(c(rep("treat", 4), rep("control", 4)))
or when I reverse the countData.
But when I set
condition <- factor(c(rep("atreat", 4), rep("control", 4)))
my head(res) gives
log2 fold change (MAP): condition ctrl vs atreat
Wald test p-value: condition ctrl vs atreat
So it seems that the vs comment is based on alphabetic order?
I am using DESeq2 for differential expression analysis of RNA Seq data.
My question is: which is considered "control" or "treated" in the "countData" and "condition" table.
Let me explain.
When having "countData" table in the format of "control" "control" "control" "control" "treated" "treated" "treated" "treated" table, a also assign the "condition" as follows:
condition <- factor(c(rep("control", 4), rep("treat", 4)))
Following analysis, I reach to the
res <- results(dds)
and
head(res) gives
log2 fold change (MAP): condition treat vs ctrl
Wald test p-value: condition treat vs ctrl
The exact same result I get when I reverse the "condition":
condition <- factor(c(rep("treat", 4), rep("control", 4)))
or when I reverse the countData.
But when I set
condition <- factor(c(rep("atreat", 4), rep("control", 4)))
my head(res) gives
log2 fold change (MAP): condition ctrl vs atreat
Wald test p-value: condition ctrl vs atreat
So it seems that the vs comment is based on alphabetic order?
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