DESEq2 VST error
Last seen 5.0 years ago
I'd like to perform variance stabilization transformation in DESeq2 but got this error message. Any input would be much appreciated. Thank you.
vsd <- vst(dds, blind = TRUE)
Error in vst(dds, blind = TRUE) : less than 'nsub' rows,
it is recommended to use varianceStabilizingTransformation directly
Last seen 4 weeks ago
To put more meat on my comment above, take a look at the code in the
vst function (look at
?vst and just type
vst at the console and hit return, the code will reveal itself)
You'll find that the
vst function does its magic on a subset of rows (ie. the size of the subset is equal to
nsub) then can apply it to the entire dataset.
If you call
varianceStabilizingTransform directly on your expression object
dds, it doesn't try to work on a subset of the genes in your expression matrix, and just does its thing on the whole thing.
Your problem is that your expression matrix doesn't have more than 1000 genes (rows) in it.
Last seen 3 months ago
I found that the new error message is slightly different:
Error in vst(dds, blind = TRUE, nsub = nrow(dds)) : less than 'nsub'
rows with mean normalized count > 5, it is recommended to use
In some cases, setting
nsub=nrow(dds) still didn't solve the problem because the rows with mean normalized count are less than 1000.
So it's better to check the row number by
sum( rowMeans( counts(dds, normalized=TRUE)) > 5 )
And assign this number to
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