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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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As it performs a PCA, that wouldn't really be possible. -
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, 09:12 AM.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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