error in relevel.default - 'relevel' only for (unordered) factors when setting baseline
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Yihan • 0
@8e03f28b
Last seen 7 hours 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 • 116 views
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@james-w-macdonald-5106
Last seen 6 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

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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")

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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?

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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.

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Thanks for clarifying, this is very helpful!

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