Error inDefaultAssay<-.Seurat(object =tmp, value = assay) : Cannot find assay SCT or When I try to see the cluster,=: DimPlot(object, reduction = "umap") The error: Error: Cannot find 'SCT' in this Seurat object What should I do? Thank you :)...
It is recommended to use RPCA reduction when runningFindIntegrationAnchorson large dataset by Seurat authors. However when I do this, I get error Error: Cannot find 'pca' in this Seurat What should I do to get rid of this error? should I run RunPCA beforeFindIntegrationAnchorsandScaleData?
An object of class Seurat 22131 features across 1199 samples within 1 assay Active assay: RNA (22131 features) hemivt[["percent.mt"]] <- PercentageFeatureSet(hemivt, pattern = "^MT-") VlnPlot(hemivt, features = c("nFeature_RNA", "nCount_RNA", "percent.mt"), ncol = 3, pt.size...
I am running this in a MacBook in RStudio. I already confirmed I have permissions to my output directory (I ran chmod +rw output to make sure), and I also confirmed I can run macs2 outside of R. This is how my object looks like: > chrom_assay An object of class Seurat 171904 ...
(6 batches of scRNAseq data). It works well when aggregating 2 batches of scRNAseq data only. In this regard, I caculated the variable features by other methon and pass it to seurat object directly. Clustering went well. But when I tried to run FindAllMarkers. Similar error came out:...
In short the moe object is created by SCT and integrating multiple runs of 10X. (I've removed the SCT and RNA assays as their cell count was previously not matching) moe An object of class Seurat 3000 features across 59824 samples within 1 assay ...