Question: DESeq2 vst function error
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gravatar for lenC_biotecLover
3 months ago by
lenC_biotecLover0 wrote:

Hi everyone, I have a dataset with count reads of miRNA-Seq downloaded from TCGA: on the rows I have the miRNA names and on the columns the uuid barcodes(sample names). When I launch the vst function it gets me this error:

dd = DESeqDataSetFromMatrix(d, coldata, design= ~class) 
vst = vst(dd, blind = FALSE)

Error in vst(dd, blind = FALSE) : 
  less than 'nsub' rows with mean normalized count > 5, 
  it is recommended to use varianceStabilizingTransformation directly

This is the first attempt with this package, any suggestion? Thank you so much

normalization rna-seq deseq2 R • 247 views
ADD COMMENTlink modified 3 months ago by Kevin Blighe67k • written 3 months ago by lenC_biotecLover0
0
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe67k
Republic of Ireland
Kevin Blighe67k wrote:

Your dataset is small (< 1000 variables) and / or has a low number of expressed genes. Either way, the problem can be mitigated by using varianceStabilizingTransformation(), or just re-use vst() and set a lower value for nsub.

Type ?vst to see what is happening with the nsub parameter.

Kevin

ADD COMMENTlink written 3 months ago by Kevin Blighe67k

I set a lower number, and it works, thank you! My dataset has 1800 miRNAs. This does mean that only few of them are considered for the calculation? How does the algorithm operates in this cases?

ADD REPLYlink modified 3 months ago • written 3 months ago by lenC_biotecLover0
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