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LTLA / batchelor

Clone of the Bioconductor repository for the batchelor package.
https://bioconductor.org/packages/devel/bioc/html/batchelor.html
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more singular values/vectors requested than available #40

Open sailseem opened 1 year ago

sailseem commented 1 year ago

Dear Developer,

I wanna ask about an error occurred when I run the fastMNN

out <- fastMNN(sce, batch = sce$Batch,

  • auto.merge = TRUE,
  • subset.row = rowData(sce)$use_channel,
  • assay.type = "exprs") Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth = TRUE, : You're computing too large a percentage of total singular values, use a standard svd instead. Warning message: In check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - : more singular values/vectors requested than available

Can you help me figure that out? Thanks in advance!

LTLA commented 1 year ago

Looks like it's just a warning. By default, fastMNN() computes 50 PCs, but you have fewer than 50 features, so it can't actually compute 50 PCs. IIRC it just falls back to computing however many PCs it can, so you can just keep on going with your analysis.