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Irrationone / cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data
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error when using raw count matrix as input #23

Closed ywang65 closed 5 years ago

ywang65 commented 5 years ago

Hi,

I encountered some problem when using raw count matrix as the input. I just used the example_sce and example_rho in the example. So my code is cellassign(t(counts(example_sce)),example_rho) and it shows:

No size factors supplied - computing from matrix. It is highly recommended to supply size factors calculated using the full gene set 20 NaN Error in while (mi < max_iter_adam && Q_diff > rel_tol_adam) { : missing value where TRUE/FALSE needed In addition: Warning message: In .local(x, ...) : encountered negative size factor estimates

What should I do for this? Thanks!

kieranrcampbell commented 5 years ago

Hi @ywang65

Looks like scran is returning negative size factors, which isn't ideal. If I remember rightly, scran's algorithm is inherently random, so this may be stochastic.

To solve this, consider a different size factor calculation e.g. edgeR size factors:

sf <- edgeR::calcNormFactors(counts(example_sce))

stopifnot(all(sf > 0))

cellassign(t(counts(example_sce)),example_rho, sf)

Does that fix things?

ywang65 commented 5 years ago

Yes, it works. Thank you very much!

From: Kieran R Campbell notifications@github.com Reply-To: Irrationone/cellassign reply@reply.github.com Date: Tuesday, February 19, 2019 at 4:49 PM To: Irrationone/cellassign cellassign@noreply.github.com Cc: "Wang,Yuanxin" YWang65@mdanderson.org, Mention mention@noreply.github.com Subject: [EXT] Re: [Irrationone/cellassign] error when using raw count matrix as input (#23)

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Hi @ywang65https://github.com/ywang65

Looks like scran is returning negative size factors, which isn't ideal. If I remember rightly, scran's algorithm is inherently random, so this may be stochastic.

To solve this, consider a different size factor calculation e.g. edgeR size factors:

sf <- edgeR::calcNormFactors(counts(example_sce))

stopifnot(all(sf > 0))

cellassign(t(counts(example_sce)),example_rho, sf)

Does that fix things?

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