Mean-Variance Plot for Normalised Counts
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 1 day ago
Australia

A SeqExpressionSet can store unnormalised counts and normalised counts, but it only seems to be possible to plot the unnormalised counts by meanVarPlot. It would be useful to be able to plot normalised counts to visualise the effect of applying a normalisation method (e.g. DESeq2's varianceStabilizingTransformation) to the count data set (i.e. is it visibly homoscedastic once it's transformed?). Also, if a SeqExpressionSet is created by newSeqExpressionSet, there is a table of NA created in set@assayData named normalizedCounts. If a table of normalised values is added later by using normCounts(set) <- measurementsVST, then an element named normCounts is added to set@assayData. So there are two tables for normalised values simultaneously in assayData. Can this inconsistency be resolved?

EDASeq meanVarPlot • 377 views
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Entering edit mode
davide risso ▴ 870
@davide-risso-5075
Last seen 5 months ago
University of Padova

This is a bug and should be fixed. I'll take care of this ASAP.

normCounts(set) <- measurementsVST should store the normalized counts in the normalizedCounts slot.

The meanVarPlot function uses the normalized counts, if available. But of course it looks for it as normalizedCounts not normCounts. So fixing the bug will also make the behavior of the function what you expect.

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