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Question: ntop parameter in plotPCA(). DESeq2
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gravatar for Mthabisi Moyo
3 months ago by
Mthabisi Moyo10 wrote:

Given that the PCA plot is likely to change somewhat depending on the number of genes you decide to specify with the ntop parameter, are there any recommendations on how to best set this value besides arbitrarily setting it at the default of 500/1000? Could including all genes have a negative effect if a lot of the genes have low variance?

Thanks!

 

ADD COMMENTlink modified 3 months ago by Michael Love19k • written 3 months ago by Mthabisi Moyo10
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gravatar for Michael Love
3 months ago by
Michael Love19k
United States
Michael Love19k wrote:

"Could including all genes have a negative effect if a lot of the genes have low variance?"

Not really. The low count noise is dealt with by vst() or rlog(). It's up to you what ntop to choose, choosing a small-ish number, e.g. 500, focuses the PCA plot on the most variable genes across samples, which is often the DE genes across condition (although this information is not used to pick the genes in the PCA plot).

ADD COMMENTlink written 3 months ago by Michael Love19k
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