Question

error in relevel.default - 'relevel' only for (unordered) factors when setting baseline

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Yihan • 0

@8e03f28b

Last seen 3.3 years ago

United States

I'm trying to use relevel to set the baseline to "WT" by specifying the reference level

Code should be placed in three backticks as shown below


keep <- rowSums(counts(ddsHTSeq)) >= 10
ddsHTSeq_filtered <- ddsHTSeq[keep,]

ddsHTSeq_filtered$Genotype <- relevel(ddsHTSeq_filtered$Genotype, ref = "WT")


> Error in relevel.default(ddsHTSeq_filtered$Genotype, ref = "WT") :   
> 'relevel' only for (unordered) factors

Here is what the sample sheet/table looks like. This genotype is divided into "mdx" and "WT" on the 3rd column.

DESeq2 • 8.4k views

ADD COMMENT • link 3.5 years ago Yihan • 0

score 0 · Answer 1 · 2021-07-13

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 hours ago

United States

If you are dispatching on relevel.default, it's because your input isn't already a factor. You can make it a factor and also specify the baseline at the same time. See ?factor

ADD COMMENT • link 3.5 years ago James W. MacDonald 67k

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The code before I did relevel is this. Did it fail to make factors?

ddsHTSeq_filtered$group <- factor(paste0(ddsHTSeq_filtered$Age, ddsHTSeq_filtered$Genotype, ddsHTSeq_filtered$Tissue))

ddsHTSeq_filtered$Genotype <- relevel(ddsHTSeq_filtered$Genotype, ref = "WT")

ADD REPLY • link 3.5 years ago Yihan • 0

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The code you present does nothing to the Genotype column that you then try to relevel. So yes, it made a factor for the combined Age, Gentotype, Tissue group, but why do you think that would affect the Genotype column?

ADD REPLY • link 3.5 years ago James W. MacDonald 67k

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To clarify, this line

ddsHTSeq_filtered$group <- factor(paste0(ddsHTSeq_filtered$Age, ddsHTSeq_filtered$Genotype, ddsHTSeq_filtered$Tissue))

adds a new 'group' column to your ddsHTSeq_filtered object by pasteing three existing columns together. But it doesn't do anything to those three other columns.