plotMA (DESeq2) Issue
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ap_vc21 • 0
@ap_vc21-15142
Last seen 3.6 years ago

I am following the standard RNA-seq analysis workflow to make sense of some experimental data, using the DESeq2 package. Here is the MA-plot I have:

I am not concerned about the low log-fold change, but this looks a bit weird, since I would have expected the major part of the genes to be found in the low counts range.

I followed the standard pipeline for this analysis. Is there any obvious reason why I am having this kind of result?

Thank you.

deseq2 plotMA rnaseq logfoldchange • 610 views
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@mikelove
Last seen 23 hours ago
United States

Sorry, what is not expected here? DESeq2 moderates the LFC from genes with little to no information for accurately estimating the LFC. Please see the DESeq2 paper or the vignette section on LFC shrinkage.

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I am quite new to the field, so I am very open to be totally mistaken. The shrinkage in the LFC in the low counts range has to considered as normal then? 

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Take a look at the paper and the vignette. You will find the same kind of plots there. Again, it is expected.

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