Question: DESEq2 VST error
gravatar for anpham
20 months ago by
anpham0 wrote:

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


ADD COMMENTlink modified 20 months ago • written 20 months ago by anpham0

how many rows are in your dds? ie. what is the output of nrow(dds)?

ADD REPLYlink written 20 months ago by Steve Lianoglou12k

Thank you, you're right. This is a miRNA dataset so there are 767 rows. Would I have another option to do VST with this number of rows? 

ADD REPLYlink written 20 months ago by anpham0

The default number of rows for vst() is nsub=1000. You can just set nsub=nrow(dds), or you can use the function that is recommended by name in the error message.

ADD REPLYlink written 20 months ago by Michael Love22k
Answer: DESEq2 VST error
gravatar for Steve Lianoglou
20 months ago by
Steve Lianoglou12k wrote:

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.

ADD COMMENTlink written 20 months ago by Steve Lianoglou12k
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