Hi Japrin
When running your vignette, in the block #All in One: sce.Pollen <- ssc.run(sce.Pollen,method.vgene = "sd",sd.n = 1500,method.reduction = "pca",method.clust = "kmeans", k.batch=11,seed = 9997) yields the error message Error in ssc.reduceDim(obj, assay.name = assay.name, method = method.reduction, : No variable genes identified by method sd !
It could be solved by rewriting the argument value for method.vgene from "sd" to "HVG.sd", so running
sce.Pollen <- ssc.run(sce.Pollen,method.vgene = "HVG.sd",sd.n = 1500,method.reduction = "pca",method.clust = "kmeans", k.batch=11,seed = 9997)
which then works: this makes sense, as in the invoked ssc.variableGene method, the arguments can be one of "HVG.sd", "HVG.mean.sd", "HVG.trendVar" (but not "sd").
Is this the correct way of running this vignette?
Kind regards
Hi Japrin
When running your vignette, in the block #All in One:
sce.Pollen <- ssc.run(sce.Pollen,method.vgene = "sd",sd.n = 1500,method.reduction = "pca",method.clust = "kmeans", k.batch=11,seed = 9997)yields the error messageError in ssc.reduceDim(obj, assay.name = assay.name, method = method.reduction, : No variable genes identified by method sd !It could be solved by rewriting the argument value for method.vgene from
"sd"to"HVG.sd", so runningsce.Pollen <- ssc.run(sce.Pollen,method.vgene = "HVG.sd",sd.n = 1500,method.reduction = "pca",method.clust = "kmeans", k.batch=11,seed = 9997)which then works: this makes sense, as in the invoked
ssc.variableGenemethod, the arguments can be one of"HVG.sd","HVG.mean.sd","HVG.trendVar"(but not"sd").Is this the correct way of running this vignette?
Kind regards