Handling biological replicates in DESeq2
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sk • 0
@fa435831
Last seen 2 days ago
Canada

I have 4 biological replicates of mRNA samples. For my dds, I am comparing type but have also added in the replicate factor to account for the biological replicates.

Is this correct? I have a column specifying the replicate number (1, 2, 3, or 4) per sample as they do not have the same names.

dds <- DESeqDataSetFromMatrix(
  countData = counts_data,
  colData = metadata,
  design = ~ Replicate + Type  # accounting for biological replicates
)
DESeq2 • 581 views
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ATpoint ★ 4.6k
@atpoint-13662
Last seen 2 days ago
Germany

Generally, you don't have to include the replication information since the software will consider all elements of dds$Type that have the same factor level as replicates for this group. It can sometimes make sense to include the replicate information, for example if every replicate is a different batch, so essentially replicate would be the same as batch, and there is evidence, for example in PCA, that batch is driving unwanted variation. If not, don't include.

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swbarnes2 ★ 1.4k
@swbarnes2-14086
Last seen 2 days ago
San Diego

Go read the vignette. They don't include replicate.

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