Cannot find lsi in this seurat object
WebNov 15, 2024 · I've traced the issue to within SelectIntegrationFeatures and when var.features is filtered by whether or not they appear in the raw data for both objects - this cuts the length of var.features below the length of nfeatures set in the initial call of FindIntegrationAnchors.This then causes tie.val to be NA, and for 0 features to be …
Cannot find lsi in this seurat object
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WebFeb 11, 2024 · object = P2dual, nn.name = "wknn", assay = "RNA", verbose = TRUE ) Warning: The following arguments are not used: reduction.model, return.model, n.neighbors, set.op.mix.ratio, … WebDec 16, 2024 · Error: Cannot find 'pca' in this Seurat object use the 1st 'so' object (Seurat object) from running the code provided on the UCSC Cell browser website try running PCA directly on the above without running any of the intervening analysis in the vignette. OR: start from the raw data (exprMatrix.tsv.gz) then:
WebApr 30, 2024 · T0_R.markers <- FindMarkers (immune.combined.sct, assay = "SCT", ident.1 = "naive", ident.2 = "NR", Error in WhichCells.Seurat (object = object, idents = ident.1) : Cannot find the following identities in the object: naive head (x=Idents (object = immune.combined.sct) WebJun 19, 2024 · Maybe you can try Seurat::AddModuleScore (), then FeaturePlot () and see if some of your B cells are different. After plotting this on GenePlot (), perhaps you can set a cutoff, then assign identities. Alternatively, use your B cell gene list in RunPCA (object, pc.genes = yourgenelist) instead of the usual variable genes.
WebAug 10, 2024 · I have 9 single cell samples that I combined in a loop for object "pbmc.f" An object of class Seurat 27000 features across 50929 samples within 1 assay Active assay: RNA (27805 features) 2 dimensional reductions calculated: pca, umap WebOct 26, 2024 · You can extract the necessary values and add them directly the plot as a second layer using plot + geom_text().This is very similar to the inner workings of the DimPlot function with label = TRUE but allows you to use anything as label. # I use dplyr v1.0.2 for all data frame manipulations # First the cluster annotation and the tsne …
WebMar 3, 2024 · It is recommended to use RPCA reduction when running FindIntegrationAnchors on large dataset by Seurat authors. However when I do this, I …
Webobject.list: A list of Seurat objects between which to find anchors for downstream integration. assay: A vector of assay names specifying which assay to use when constructing anchors. If NULL, the current default assay for each object is used. reference: A vector specifying the object/s to be used as a reference during integration. cpzonlle スマホWebMar 2, 2024 · Right. It seems that not all individual objects in your pag.combined_batches have ref.umap. Could you find which object doesn't have ref.umap? Additionally, If it is ok for you, i would suggest you send the objects to me and it may be easier for me to find the bugs. my email: [email protected] magnolia gyn hammond laWebobject. An object... Arguments passed to other methods and IRLBA. assay. Name of Assay PCA is being run on. npcs. Total Number of PCs to compute and store (50 by default) rev.pca. By default computes the PCA on the cell x gene matrix. Setting to true will compute it on gene x cell matrix. weight.by.var magnolia gun shopWebMar 23, 2024 · Seurat offers two workflows to identify molecular features that correlate with spatial location within a tissue. The first is to perform differential expression based on pre-annotated anatomical regions within the tissue, which may be determined either from unsupervised clustering or prior knowledge. cpz modelWebDec 18, 2024 · Hi, I'm excited to use the new integration with UMAP but I can't get it to work. Below is the R code and verification that it is installed. > scRNAseq.integrated <- RunUMAP(object = scRNAseq.integrated, reduction = "pca", dims = 1:30) Er... cpzrcl2Web#' @slot dir_path_SingCellR_object_files contains the directory name that contains SingCellaR objects from multiple individual sample. #' @slot SingCellR_object_files contains the vector of individual object names. #' @slot Variable.genes contains the list of identified variable genes. cp zona centro leon gtoWebSeurat object to use as the reference. query. Seurat object to use as the query. normalization.method. Name of normalization method used: LogNormalize or SCT. ... If reduction = "lsiproject", the stored LSI dimension reduction in the reference object is used to project the query dataset onto the reference. cpzp unicov