Hello, I am following Seurat's pipeline https://satijalab.org/seurat/v3.0/immune_alignment.html for integrating cross-specie data.
In the code below, object.list inputs a list of Seurat objects.It gives warning:
skin.anchors <- FindIntegrationAnchors(object.list = list(skin2, skin3,neoskin))
Warning message: In RunCCA.Seurat(object1 = object.1, object2 = object.2, ... : Fewer than 50 features used as input for CCA. Requested number is larger than the number of available items (3). Setting to 3. X 50
Then following output by IntegrateData() function:
> skin.integrated <- IntegrateData(anchorset = skin.anchors, dims = 1:30)
Merging dataset 2 into 1 Extracting anchors for merged samples Finding integration vectors Warning in irlba(A = t(x = object), nv = npcs, ...) : You're computing too large a percentage of total singular values, use a standard svd instead. Finding integration vector weights Error in Embeddings(reduction)[nn.cells2, dims] : subscript out of bounds
Can anyone please help resolving the error? Thank You in advance!