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Old 06-16-2014, 03:02 PM   #1
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Default DESeq2 plotPCA combine replicates

By default, the plotPCA function in DESeq2 plots the replicates separately. Is there a way to combine replicates so that there is only one dot per group? There does not seem a built-in option for that and it's not obvious to me by looking at the source.
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Old 06-17-2014, 01:34 AM   #2
Devon Ryan
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As it performs a PCA, that wouldn't really be possible.
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Old 06-17-2014, 09:53 AM   #3
Michael Love
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hi id0,

There is a collapseReplicates() function in DESeq2 if you want to combine technical replicates.

... and you could create a new DESeqDataSet with this just for plotting.

Last edited by Michael Love; 06-17-2014 at 10:12 AM.
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