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VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
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Error in PlotRelativeExpression functions #66

Open hkarakurt8742 opened 1 year ago

hkarakurt8742 commented 1 year ago

Hello everyone, I am using Sierra and I keep getting this error for all PlotRelativeExpression functions (TSNE, UMAP, Box).

error in apply(expression.set, 1, function(x) { : dim(x) must have a positive length

I checked my Sierra object and everything looks okay. I completed the DUTest without any problem. I also converted my counts in Sierra Object via as.matrix() function but nothing changed.

What might be the problem?

Thank you in advance.

rj-patrick commented 11 months ago

Hi @hkarakurt8742,

Sorry for the slow response. Could you check the active Idents in your Seurat object? This is what Sierra relies on to generate the relative expression and I suspect the most likely cause of that error message is a problem with subsetting the data by cell cluster/class identity.